bluuebunny/crossref_metadata_2025 huggingface dataset:
What can lotteries do for education?
Authors: Stone Peter
Published: October 2008

England's new School Admissions Code endorses the use of lotteries to admit students to oversubscribed schools. Is this endorsement wise? This article argues that lotteries make decision-making without regard to reasons possible. This sanitizing effect is desirable in order to protect against bad reasons. This effect could make at least four distinct contributions to school admission arrangements.The most important of these contributions is the ability of lotteries to ensure impartiality , an essential component of justice.Whether these contributions justify resort to admission by lottery, however, depends upon the circumstances under which admission must take place, and these circumstances are likely to be controversial in real-life cases.
`White privilege': A mild critique1
Authors: Blum Lawrence
Published: October 2008

White privilege analysis has been influential in philosophy of education. I offer some mild criticisms of this largely salutary direction — its inadequate exploration of its own normative foundations, and failure to distinguish between `spared injustice', `unjust enrichment' and `non-injustice-related' privileges; its inadequate exploration of the actual structures of racial disparity in different domains (health, education, wealth); its tendency to deny or downplay differences in the historical and current experiences of the major racial groups; its failure to recognize important ethnic differences within racial groups; and its overly narrow implied political project that omits many ways that White people can contribute meaningfully to the cause of racial justice.
The status of the subject in the classroom community of inquiry
Authors: Šimenc Marjan
Published: October 2008

This article deals with the issue of how to establish an authentic community of inquiry. I propose the introduction of a distinction between two stages of the community of inquiry: the stage of an emergent community of inquiry and the stage of an established community of inquiry. Further on, I propose an analysis of the structure of intentions and goals in the community of inquiry using Elster's concept of `states that are essentially by-products'. I suggest that the position of the subject be defined on the basis of the aforementioned two stages of the community: in the first stage, there is a community consisting of equal individuals who voluntarily engage in dialogue, whereas in the second stage there is a subject who is not engaged in dialogue, but arises in it at a certain point. It seems that it is the internalized dialogical community, in which the participants are equal and strive for clarity and transparency, that generates the necessary space for the particular foundation of the subject to show itself — the particular foundation that is not yet captured in reflection and that defies articulation in dialogue.
Cardinal virtues of academic administration
Authors: Curren Randall
Published: October 2008

The aim of this article is to articulate the basic elements of a comprehensive ethic of academic administration, organized around a set of three cardinal virtues: commitment to the good of the institution; good administrative judgment; and conscientiousness in discharging the duties of the office. In addition to explaining this framework and defending its adequacy, the article develops an account of the nature of integrity, and argues that the three cardinal virtues of academic administration can be captured in the concept of integrity in academic administration.The Aristotelian basis for this framework is summarized, and its central ideas are illustrated through a variety of applications.
Development of Initial and Advanced Standards of Knowledge and Skills for Teachers of Children Who Are Deaf or Hard of Hearing
Authors: Easterbrooks Susan R. , Putney LaTisha L.
Published: October 2008

In 1989, the delegate assembly of the Council for Exceptional Children began the process of developing standards of knowledge and skills for all beginning teachers of special education, including teachers of children who are deaf or hard of hearing. Now in its third major revision, these standards provide guidance to states' departments of education and to teacher preparation programs both nationally and internationally. This article provides a brief chronology of the process and presents a discussion of the most recent revalidation sequence. Two companion articles present the new standards for initial teacher preparation and advanced teacher preparation, including the evidence base in support of the standards' statements.
Knowledge and Skills for Teachers of Individuals Who Are Deaf and Hard of Hearing
Authors: Easterbrooks Susan R.
Published: October 2008

The Council for Exceptional Children and the Council on Education of the Deaf have worked together for over a decade to maintain mutually agreed upon standards for teachers of children who are deaf and hard of hearing. This article presents the newly developed and validated standards of knowledge and skills for teachers who are working on advanced preparation in their programs in deaf education. This is the third article in a set of companion pieces describing the process and outcomes of the most recent rounds of development, validation, and revalidation.
Knowledge and Skills for Teachers of Individuals Who Are Deaf or Hard of Hearing
Authors: Easterbrooks Susan R.
Published: October 2008

The Council for Exceptional Children and the Council on the Education of the Deaf have worked together for over a decade to maintain mutually agreed on standards for teachers of children who are deaf or hard of hearing. This article presents the updated and revalidated standards of knowledge and skills for teachers in their initial preparation programs in deaf education. In addition, the article provides the evidence base in support of these standards.
Towards a Theoretical Model of Performance Inhibiting Workplace Dynamics
Authors: Altman Brian A. , Akdere Mesut
Published: October 2008

A construct and model of performance inhibiting workplace dynamics is introduced to conceptualize the adverse consequences on performance and quality of certain interpersonal interactions in the workplace and behavioral instructions leading to double binds. Results of a literature review are presented which provide evidence for the existence of a set of workplace interactions that are associated with reduced performance and quality. It is hypothesized that the negative influences on employee performance in the model occur by alteration of one or more of the following three of Swanson's performance variables at the individual level: mission/goal, capacity, or motivation. As a field that considers performance as an important outcome of its practice, human resource development scholars and practitioners need to understand such dynamics in order to eliminate or reduce their effects on employee performance.
Integrative Literature Review: Methods in Identifying Exemplary Performance: A Review of the Literature and Implications for HRD
Authors: Smith Terri Freeman
Published: October 2008

This literature review provides an analysis of relevant ASTD (American Society for Training & Development) competency studies in Workplace Learning and Performance (WLP) and other research findings related to the methodology used in identifying exemplary and average performers. These findings helped create the research model and methods used in the qualitative data collection for the rubric used for the CPLP (Certified Professional in Learning and Performance) pilot exam. This chronicle is for those who seek out a method of collection of exemplary status behaviors within their organizations.
Bringing the Republic to life
Authors: Brooks Thom
Published: October 2008

I have taught Plato's Republic for several years although seminars on this text can be difficult and pose certain challenges, most especially with first year students new to university: the ancient Greeks seem a long way from the technocratic society we live in today. More importantly, the complexity of our relationship to each other as citizens and to the state has grown increasingly since the ancient world as well. Students find this revered book full of unfamiliar names, arguments, and styles of presentation and immediately become a bit frustrated. In this article, I provide a thorough, concrete example of how I have attempted to overcome this problem in my work using the seminar format. I have learned some useful tips for tackling this text and hope this article might be useful to others grappling with the teaching of abstract concepts and texts, opening the door for students to engage with a new civic awareness.
Democracy and robust hope
Authors: Singh Michael , Sawyer Wayne
Published: October 2008

A key aim of democratic public policy should be the provision of hope. It is often argued that a key element of hope is not only a drive for equity in the face of neo-liberal marketization, but also the opportunity for the practice of agency by (especially disadvantaged) citizens. Here we examine the relationship between democracy and hope in an educational context by discussing recent education and training reforms `for the future' (ETRF) in the Australian state of Queensland. We argue that these reforms have provided the opportunity for active democratic participation by young people and their communities in planning their futures and that they therefore provide an instance of what we have called `robust hope'.
Can schooling contribute to a more just society?
Authors: Apple Michael W.
Published: October 2008

This article combines discussions of the politics of education with personal story telling to remind us why the continuing struggle over schooling — over what is and is not taught, over how it is taught and evaluated, over how students with different characteristics are treated, over how teachers and other school employees are respectfully dealt with, over how the relationship between schools and their communities can be democratized, and so much more — is absolutely crucial to the pursuit of social justice. Using the example of the book Democratic Schools , it suggests tactics for making critically democratic practices more visible. It also describes seven specific tasks that critical scholar/activists in education should perform if we are committed to challenging dominant relations in education and the larger society.
The politics of shame in intercultural education
Authors: Zembylas Michalinos
Published: October 2008

Against a perspective of shame that would see it as something paralyzing, negative and destructive, I draw out a different account of the politics of shame in intercultural education. I explore the openings that are created for a productive politics of shame in the context of discussions surrounding intercultural education via tracing how different kinds of shame are evoked or rejected in collective imagination — both in politics and in education. My goal is to show that a rehabilitation of the political and ethical value of shame challenges the opposition between self and other, and that this act can be beneficial, particularly in educational settings. An effort to transcend the usual dichotomies around the pride/shame debate both in political and in educational discourses will tackle the cultural, political and educational uses of shame and help educators gain a deeper understanding of the meaning and implications of shame in intercultural education.
Discovery of dominant and dormant genes from expression data using a novel generalization of SNR for multi-class problems
Authors: Tsai Yu-Shuen , Lin Chin-Teng , Tseng George C , Chung I-Fang , Pal Nikhil Ranjan
Published: October 2008

Background

The Signal-to-Noise-Ratio (SNR) is often used for identification of biomarkers for two-class problems and no formal and useful generalization of SNR is available for multiclass problems. We propose innovative generalizations of SNR for multiclass cancer discrimination through introduction of two indices, Gene Dominant Index and Gene Dormant Index (GDIs). These two indices lead to the concepts of dominant and dormant genes with biological significance. We use these indices to develop methodologies for discovery of dominant and dormant biomarkers with interesting biological significance. The dominancy and dormancy of the identified biomarkers and their excellent discriminating power are also demonstrated pictorially using the scatterplot of individual gene and 2-D Sammon's projection of the selected set of genes. Using information from the literature we have shown that the GDI based method can identify dominant and dormant genes that play significant roles in cancer biology. These biomarkers are also used to design diagnostic prediction systems.

Results and discussion

To evaluate the effectiveness of the GDIs, we have used four multiclass cancer data sets (Small Round Blue Cell Tumors, Leukemia, Central Nervous System Tumors, and Lung Cancer). For each data set we demonstrate that the new indices can find biologically meaningful genes that can act as biomarkers. We then use six machine learning tools, Nearest Neighbor Classifier (NNC), Nearest Mean Classifier (NMC), Support Vector Machine (SVM) classifier with linear kernel, and SVM classifier with Gaussian kernel, where both SVMs are used in conjunction with one-vs-all (OVA) and one-vs-one (OVO) strategies. We found GDIs to be very effective in identifying biomarkers with strong class specific signatures. With all six tools and for all data sets we could achieve better or comparable prediction accuracies usually with fewer marker genes than results reported in the literature using the same computational protocols. The dominant genes are usually easy to find while good dormant genes may not always be available as dormant genes require stronger constraints to be satisfied; but when they are available, they can be used for authentication of diagnosis.

Conclusion

Since GDI based schemes can find a small set of dominant/dormant biomarkers that is adequate to design diagnostic prediction systems, it opens up the possibility of using real-time qPCR assays or antibody based methods such as ELISA for an easy and low cost diagnosis of diseases. The dominant and dormant genes found by GDIs can be used in different ways to design more reliable diagnostic prediction systems.
Mining protein networks for synthetic genetic interactions
Authors: Paladugu Sri R , Zhao Shan , Ray Animesh , Raval Alpan
Published: October 2008

Background

The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is therefore of interest to extend this observation and examine whether network properties of two proteins considered simultaneously can determine their joint dispensability, i.e., their propensity for synthetic sick/lethal interaction. Accordingly, we examine the predictive power of protein interaction networks for synthetic genetic interaction in Saccharomyces cerevisiae, an organism in which high confidence protein interaction networks are available and synthetic sick/lethal gene pairs have been extensively identified.

Results

We design a support vector machine system that uses graph-theoretic properties of two proteins in a protein interaction network as input features for prediction of synthetic sick/lethal interactions. The system is trained on interacting and non-interacting gene pairs culled from large scale genetic screens as well as literature-curated data. We find that the method is capable of predicting synthetic genetic interactions with sensitivity and specificity both exceeding 85%. We further find that the prediction performance is reasonably robust with respect to errors in the protein interaction network and with respect to changes in the features of test datasets. Using the prediction system, we carried out novel predictions of synthetic sick/lethal gene pairs at a genome-wide scale. These pairs appear to have functional properties that are similar to those that characterize the known synthetic lethal gene pairs.

Conclusion

Our analysis shows that protein interaction networks can be used to predict synthetic lethal interactions with accuracies on par with or exceeding that of other computational methods that use a variety of input features, including functional annotations. This indicates that protein interaction networks could plausibly be rich sources of information about epistatic effects among genes.
Fgfr1 signalling in the development of a sexually selected trait in vertebrates, the sword of swordtail fish
Authors: Offen Nils , Blum Nicola , Meyer Axel , Begemann Gerrit
Published: October 2008

Background

One of Darwin's chosen examples for his idea of sexual selection through female choice was the "sword", a colourful extension of the caudal fin of male swordtails of the genus Xiphophorus. Platyfish, also members of the genus Xiphophorus, are thought to have arisen from within the swordtails, but have secondarily lost the ability to develop a sword. The sustained increase of testosterone during sexual maturation initiates sword development in male swordtails. Addition of testosterone also induces sword-like fin extensions in some platyfish species, suggesting that the genetic interactions required for sword development may be dormant, rather than lost, within platyfish. Despite considerable interest in the evolution of the sword from a behavioural or evolutionary point of view, little is known about the developmental changes that resulted in the gain and secondary loss of the sword. Up-regulation of msxC had been shown to characterize the development of both swords and the gonopodium, a modified anal fin that serves as an intromittent organ, and prompted investigations of the regulatory mechanisms that control msxC and sword growth.

Results

By comparing both development and regeneration of caudal fins in swordtails and platyfish, we show that fgfr1 is strongly up-regulated in developing and regenerating sword and gonopodial rays. Characterization of the fin overgrowth mutant brushtail in a platyfish background confirmed that fin regeneration rates are correlated with the expression levels of fgfr1 and msxC. Moreover, brushtail re-awakens the dormant mechanisms of sword development in platyfish and activates fgfr1/msxC-signalling. Although both genes are co-expressed in scleroblasts, expression of msxC in the distal blastema may be independent of fgfr1. Known regulators of Fgf-signalling in teleost fins, fgf20a and fgf24, are transiently expressed only during regeneration and thus not likely to be required in developing swords.

Conclusion

Our data suggest that Fgf-signalling is involved upstream of msxC in the development of the sword and gonopodium in male swordtails. Activation of a gene regulatory network that includes fgfr1 and msxC is positively correlated with fin ray growth rates and can be re-activated in platyfish to form small sword-like fin extensions. These findings point towards a disruption between the fgfr1/msxC network and its regulation by testosterone as a likely developmental cause for sword-loss in platyfish.
Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome
Authors: Moisy Cédric , Garrison Keith E , Meredith Carole P , Pelsy Frédérique
Published: October 2008

Background

Retrotransposons make a significant contribution to the size, organization and genetic diversity of their host genomes. To characterize retrotransposon families in the grapevine genome (the fourth crop plant genome sequenced) we have combined two approaches: a PCR-based method for the isolation of RnaseH-LTR sequences with a computer-based sequence similarity search in the whole-genome sequence of PN40024.

Results

Supported by a phylogenic analysis, ten novel Ty1/copia families were distinguished in this study. To select a canonical reference element sequence from amongst the various insertions in the genome belonging to each retroelement family, the following screening criteria were adopted to identify the element sequence with: (1) perfect 5 bp-duplication of target sites, (2) the highest level of identity between 5' and 3'-LTR within a single insertion sequence, and (3) longest, un-interrupted coding capacity within the gag-pol ORF. One to eight copies encoding a single putatively functional gag-pol polyprotein were found for three families, indicating that these families could be still autonomous and active. For the others, no autonomous copies were identified. However, a subset of copies within the presumably non-autonomous families had perfect identity between their 5' and 3' LTRs, indicating a recent insertion event. A phylogenic study based on the sequence alignment of the region located between reverse transcriptase domains I and VII distinguished these 10 families from other plant retrotransposons. Including the previously characterized Ty1/copia-like grapevine retrotransposons Tvv1 and Vine 1 and the Ty3/gypsy-like Gret1 in this assessment, a total of 1709 copies were identified for the 13 retrotransposon families, representing 1.24% of the sequenced genome. The copy number per family ranged from 91–212 copies. We performed insertion site profiling for 8 out of the 13 retrotransposon families and confirmed multiple insertions of these elements across the Vitis genus. Insertional polymorphism analysis and dating of full-length copies based on their LTR divergence demonstrated that each family has a particular amplification history, with 71% of the identified copies being inserted within the last 2 million years.

Conclusion

The strategy we used efficiently delivered new Ty1/copia-like retrotransposon sequences, increasing the total number of characterized grapevine retrotrotransposons from 3 to 13. We provide insights into the representation and dynamics of the 13 families in the genome. Our data demonstrated that each family has a particular amplification pattern, with 7 families having copies recently inserted within the last 0.2 million year. Among those 7 families with recent insertions, three retain the capacity for activity in the grape genome today.
Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function
Authors: Tran Hoa T , Krushkal Julia , Antommattei Frances M , Lovley Derek R , Weis Robert M
Published: October 2008

Background

Geobacterspecies are δ-Proteobacteriaand are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth ofGeobacterin changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established forEscherichia colichemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand howGeobacterthrives in natural environments and better their use in microbial fuel cells.

Results

The genomes ofG. sulfurreducens, G. metallireducens, andG. uraniireducenscontain multiple (~70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster ofE. coli, theGeobacterclusters are not all located near the flagellar genes. The probable functions of someGeobacterclusters are assignable by homology to known pathways; others appear to be unique to theGeobactersp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression inGeobacterdiffers fromE. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors σ28and σ54play a role in regulating theGeobacterchemotaxis gene expression.

Conclusion

The numerous chemoreceptors and chemotaxis-like gene clusters ofGeobacterappear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways.
Disturbances in metabolic, transport and structural genes in experimental colonic inflammation in the rat: a longitudinal genomic analysis
Authors: Martínez-Augustin Olga , Merlos Manel , Zarzuelo Antonio , Suárez María Dolores , de Medina Fermín Sánchez
Published: October 2008

Background

Trinitrobenzenesulphonic acid (TNBS) induced rat colitis is one of the most widely used models of inflammatory bowel disease (IBD), a condition whose aetiology and pathophysiology are incompletely understood. We have characterized this model at the genomic level using a longitudinal approach. Six control rats were compared with colitic animals at 2, 5, 7 and 14 days after TNBS administration (n = 3). The Affymetrix Rat Expression Array 230 2.0 system was used.

Results

TNBS-induced colitis had a profound impact on the gene expression profile, which was maximal 5 and 7 days post-induction. Most genes were affected at more than one time point. They were related to a number of biological functions, not only inflammation/immunity but also transport, metabolism, signal transduction, tissue remodeling and angiogenesis. Gene changes generally correlated with the severity of colitis. The results were successfully validated in a subset of genes by real-time PCR.

Conclusion

The TNBS model of rat colitis has been described in detail at the transcriptome level. The changes observed correlate with pathophysiological disturbances such as tissue remodelling and alterations in ion transport, which are characteristic of both this model and IBD.
Concurrent genotyping of Helicobacter pylorivirulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA
Authors: Ryberg Anna , Borch Kurt , Sun Yi-Qian , Monstein Hans-Jürg
Published: October 2008

Background

Bacterial and cellular genotyping is becoming increasingly important in the diagnosis of infectious diseases. However, difficulties in obtaining sufficient amount of bacterial and cellular DNA extracted from the same human biopsy specimens is often a limiting factor. In this study, total DNA (host and bacterial DNA) was isolated from minute amounts of gastric biopsy specimens and amplified by means of whole genome amplification using the multiple displacement amplification (MDA) technique. Subsequently, MDA-DNA was used for concurrent Helicobacter pylori and human host cellular DNA genotyping analysis using PCR-based methods.

Results

Total DNA was isolated from gastric biopsy specimens of 12 subjects with gastritis and 16 control subjects having a normal mucosa. The DNA was amplified using a multiple displacement amplification (MDA) kit. Next, concurrent genotyping was performed using H. pylori-specific virulence gene PCR amplification assays, pyrosequencing of bacterial 16S rDNA and PCR characterisation of various host genes. This includes Interleukin 1-beta (IL1B) and Interferon-gamma receptor (IFNGR1) SNP analysis, and Interleukin-1 receptor antagonist (IL1RN) variable tandem repeats (VNTR) in intron 2. Finally, regions of the vacA-gene were PCR amplified using M13-sequence tagged primers which allowed for direct DNA sequencing, omitting cloning of PCR amplicons. H. pylori specific multiplex PCR assays revealed the presence of H. pylori cagA and vacA genotypic variations in 11 of 12 gastritis biopsy specimens. Using pyrosequencing, 16S rDNA variable V3 region signatures of H. pylori were found in 11 of 12 individuals with gastritis, but in none of the control subjects. Similarly, IL1B and IFNGR1-SNP and IL1RN-VNTR patterns could be established in all individuals. Furthermore, sequencing of M13-sequence tagged vacA-PCR amplicons revealed the presence of highly diverse H. pylori vacA-s/i/m regions.

Conclusion

The PCR-based molecular typing methods applied, using MDA-amplified DNA derived from small amounts of gastric biopsy specimens, enabled a rapid and concurrent molecular analysis of bacterial and host genes in the same biopsy specimen. The principles and technologies used in this study could also be applied to any situation in which human host and microbial genes of interest in microbial-host interactions would need to be sequenced.
Development and application of the active surveillance of pathogens microarray to monitor bacterial gene flux
Authors: Stabler Richard A , Dawson Lisa F , Oyston Petra CF , Titball Richard W , Wade Jim , Hinds Jason , Witney Adam A , Wren Brendan W
Published: October 2008

Background

Human and animal health is constantly under threat by emerging pathogens that have recently acquired genetic determinants that enhance their survival, transmissibility and virulence. We describe the construction and development of an Active Surveillance of Pathogens (ASP) oligonucleotide microarray, designed to 'actively survey' the genome of a given bacterial pathogen for virulence-associated genes.

Results

The microarray consists of 4958 reporters from 151 bacterial species and include genes for the identification of individual bacterial species as well as mobile genetic elements (transposons, plasmid and phage), virulence genes and antibiotic resistance genes. The ASP microarray was validated with nineteen bacterial pathogens species, including Francisella tularensis, Clostridium difficile, Staphylococcus aureus, Enterococcus faecium and Stenotrophomonas maltophilia. The ASP microarray identified these bacteria, and provided information on potential antibiotic resistance (eg sufamethoxazole resistance and sulfonamide resistance) and virulence determinants including genes likely to be acquired by horizontal gene transfer (e.g. an alpha-haemolysin).

Conclusion

The ASP microarray has potential in the clinic as a diagnostic tool, as a research tool for both known and emerging pathogens, and as an early warning system for pathogenic bacteria that have been recently modified either naturally or deliberately.
Anaesthesia generates neuronal insulin resistance by inducing hypothermia
Authors: Holscher Christian , van Aalten Lidy , Sutherland Calum
Published: October 2008

Background

Anaesthesia is commonly employed prior to surgical investigations and to permit icv injections in rodents. Indeed it is standard practise in many studies examining the subsequent actions of hormones and growth factors on the brain. Recent evidence that the basal activity of specific intracellular signalling proteins can be affected by anaesthesia prompted us to examine the effect of anaesthesia not only on the basal activity but also the insulin sensitivity of the major insulin signalling pathways.

Results

We find that urethane- and ketamine-induced anaesthesia results in rapid activation of the phosphatidylinositol (PI) 3-kinase-protein kinase B (PKB) signalling pathway in the brain, increases tau phosphorylation while at the same time reducing basal activity of the Ras-ERK pathway. Subsequent injection of insulin does not alter the activity of either the PI 3-kinase or ERK signalling pathways, indicating a degree of neuronal molecular insulin resistance. However, if body temperature is maintained during anaesthesia then there is no alteration in the basal activity of these signalling molecules. Subsequent response of both pathways to insulin injection is restored.

Conclusion

The data is consistent with a hypothermia related alteration in neuronal signalling following anaesthesia, and emphasises the importance of maintaining the body temperature of rodents when monitoring insulin (or growth factor/neurotrophic agent) action in the brain of anesthetised rodents.
Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome
Authors: Kim Hyun-Jin , Baek Kwang-Hyun , Lee Seung-Won , Kim JungEun , Lee Bong-Woo , Cho Hye-Sun , Kim Woo Taek , Choi Doil , Hur Cheol-Goo
Published: October 2008

Background

There is no dedicated database available for Expressed Sequence Tags (EST) of the chili pepper (Capsicum annuum), although the interest in a chili pepper EST database is increasing internationally due to the nutritional, economic, and pharmaceutical value of the plant. Recent advances in high-throughput sequencing of the ESTs of chili pepper cv. Bukang have produced hundreds of thousands of complementary DNA (cDNA) sequences. Therefore, a chili pepper EST database was designed and constructed to enable comprehensive analysis of chili pepper gene expression in response to biotic and abiotic stresses.

Results

We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/.

Conclusion

The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.
Intervention, recruitment and evaluation challenges in the Bangladeshi community: Experience from a peer lead educational course
Authors: Choudhury SM , Brophy S , Fareedi MA , Zaman B , Ahmed P , Williams DRR
Published: October 2008

Background

The incidence of Type 2 diabetes is increasing worldwide and diabetes is four times more common among ethnic minority groups than among the general Caucasian population. This study reflects on the specific issues of engaging people and evaluating interventions through written questionnaires within older ethnic minority groups.

Methods

The original protocol set out to evaluate an adapted version of the X-PERT® patient program http://www.xpert-diabetes.org.uk/ using questionnaires and interviews.

Results

Questionnaires, even verbally completed, were unsuccessful and difficult to administer as participants found the questionnaire structure and design difficult to follow and did not perceive any benefit to completing the questionnaires. The benefits of attending the course were also poorly understood by participants and in many cases people participated in coming to the course as a favour to the researcher. Engaging participants required word of mouth and the involvement of active members of the community.

Conclusion

Peer led courses and their evaluation in older ethnic minority communities needs a very different approach for that in younger Caucasian patients. A structured approached to evaluation (favoured by western educational system) is inappropriate. Engaging participants is difficult and the employment of local well known people is essential.
Lysozyme M deficiency leads to an increased susceptibility to Streptococcus pneumoniae-induced otitis media
Authors: Shimada Jun , Moon Sung K , Lee Haa-Yung , Takeshita Tamotsu , Pan Huiqi , Woo Jeong-Im , Gellibolian Robert , Yamanaka Noboru , Lim David J
Published: October 2008

Background

Lysozyme is an antimicrobial innate immune molecule degrading peptidoglycan of the bacterial cell wall. Lysozyme shows the ubiquitous expression in wide varieties of species and tissues including the tubotympanum of mammals. We aim to investigate the effects of lysozyme depletion on pneumococcal clearance from the middle ear cavity.

Methods

Immunohistochemistry was performed to localize lysozyme in the Eustachian tube. Lysozyme expression was compared between the wild type and the lysozyme M-/- mice using real time quantitative RT-PCR and western blotting. Muramidase activity and bactericidal activity of lysozyme was measured using a lysoplate radial diffusion assay and a liquid broth assay, respectively. To determine if depletion of lysozyme M increases a susceptibility to pneumococal otitis media, 50 CFU of S. pneumoniae 6B were transtympanically inoculated to the middle ear and viable bacteria were counted at day 3 and 7 with clinical grading of middle ear inflammation.

Results

Immunolabeling revealed that localization of lysozyme M and lysozyme P is specific to some/particular cell types of the Eustachian tube. Lysozyme P of lysozyme M-/- mice was mainly expressed in the submucosal gland but not in the tubal epithelium. Although lysozyme M-/- mice showed compensatory up-regulation of lysozyme P, lysozyme M depletion resulted in a decrease in both muramidase and antimicrobial activities. Deficiency in lysozyme M led to an increased susceptibility to middle ear infection with S. pneumoniae 6B and resulted in severe middle ear inflammation, compared to wild type mice.

Conclusion

The results suggest that lysozyme M plays an important role in protecting the middle ear from invading pathogens, particularly in the early phase. We suggest a possibility of the exogenous lysozyme as an adjuvant therapeutic agent for otitis media, but further studies are necessary.
Odin (ANKS1A) is a Src family kinase target in colorectal cancer cells
Authors: Emaduddin Muhammad , Edelmann Mariola J , Kessler Benedikt M , Feller Stephan M
Published: October 2008

Background

Src family kinases (SFK) are implicated in the development of some colorectal cancers (CRC). One SFK member, Lck, is not detectable in normal colonic epithelium, but becomes aberrantly expressed in a subset of CRCs. Although SFK have been extensively studied in fibroblasts and different types of immune cells, their physical and functional targets in many epithelial cancers remain poorly characterised.

Results

64 CRC cell lines were tested for expression of Lck. SW620 CRC cells, which express high levels of Lck and also contain high basal levels of tyrosine phosphorylated (pY) proteins, were then analysed to identify novel SFK targets. Since SH2 domains of SFK are known to often bind substrates after phosphorylation by the kinase domain, the LckSH2 was compared with 14 other SH2s for suitability as affinity chromatography reagent. Mass spectrometric analyses of LckSH2-purified pY proteins subsequently identified several proteins readily known as SFK kinase substrates, including cortactin, Tom1L1 (SRCASM), GIT1, vimentin and AFAP1L2 (XB130). Additional proteins previously reported as substrates of other tyrosine kinase were also detected, including the EGF and PDGF receptor target Odin. Odin was further analysed and found to contain substantially less pY upon inhibition of SFK activity in SW620 cells, indicating that it is a formerly unknown SFK target in CRC cells.

Conclusion

Rapid identification of known and novel SFK targets in CRC cells is feasible with SH2 domain affinity chromatography. The elucidation of new SFK targets like Odin in epithelial cancer cells is expected to lead to novel insight into cancer cell signalling mechanisms and may also serve to indicate new biomarkers for monitoring tumor cell responses to drug treatments.
Complete clinical response of metastatic hepatocellular carcinoma to sorafenib in a patient with hemochromatosis: A case report
Authors: So Brian J , Bekaii-Saab Tanios , Bloomston Mark A , Patel Tushar
Published: October 2008

Hepatocellular carcinoma is rare, but increasing in prevalence in the United States. Recent studies have shown that sorafenib, a multikinase inhibitor, can reduce tumor progression in patients with this cancer. However, complete remission has not been observed. We report a case of a 78-year old patient with unresectable metastatic hepatocellular carcinoma who had a rapid and complete clinical response following therapy with sorafenib for six months. No evidence of disease recurrence has been noted for 6 months after discontinuation of therapy.
Idiopathic portal hypertension in an "inactive" HBV carrier: a case report
Authors: Vassiliadis Themistoklis G , Gatopoulou Anthia , Patsiaoura Kaliopi , Giouleme Olga , Soufleris Konstantinos , Boubonaris Alexandros , Katsinelos Panagiotis , Eugenidis Nikolaos
Published: October 2008

Idiopathic portal hypertension belongs to the group of non-cirrhotic portal hypertension, its etiology is still unknown but its prognosis is excellent. We report a case of 45 year old female with inactive hepatitis B virus (HBV) carrier status and persistently elevated alpha-fetoprotein (AFP), presented with features of portal hypertension and without evidence of cirrhosis or fibrosis on liver biopsy.
Recurrence dynamics does not depend on the recurrence site
Authors: Demicheli Romano , Biganzoli Elia , Boracchi Patrizia , Greco Marco , Retsky Michael W
Published: October 2008

Introduction

The dynamics of breast cancer recurrence and death, indicating a bimodal hazard rate pattern, has been confirmed in various databases. A few explanations have been suggested to help interpret this finding, assuming that each peak is generated by clustering of similar recurrences and different peaks result from distinct categories of recurrence.

Methods

The recurrence dynamics was analysed in a series of 1526 patients undergoing conservative surgery at the National Cancer Institute of Milan, Italy, for whom the site of first recurrence was recorded. The study was focused on the first clinically relevant event occurring during the follow up (ie, local recurrence, distant metastasis, contralateral breast cancer, second primary tumour), the dynamics of which was studied by estimating the specific hazard rate.

Results

The hazard rate for any recurrence (including both local and distant disease relapses) displayed a bimodal pattern with a first surge peaking at about 24 months and a second peak at almost 60 months. The same pattern was observed when the whole recurrence risk was split into the risk of local recurrence and the risk of distant metastasis. However, the hazard rate curves for both contralateral breast tumours and second primary tumours revealed a uniform course at an almost constant level. When patients with distant metastases were grouped by site of recurrence (soft tissue, bone, lung or liver or central nervous system), the corresponding hazard rate curves displayed the typical bimodal pattern with a first peak at about 24 months and a later peak at about 60 months.

Conclusions

The bimodal dynamics for early stage breast cancer recurrence is again confirmed, providing support to the proposed tumour-dormancy-based model. The recurrence dynamics does not depend on the site of metastasis indicating that the timing of recurrences is generated by factors influencing the metastatic development regardless of the seeded organ. This finding supports the view that the disease course after surgical removal of the primary tumour follows a common pathway with well-defined steps and that the recurrence risk pattern results from inherent features of the metastasis development process, which are apparently attributable to tumour cells.
Pioneer longitudinal axons navigate using floor plate and Slit/Robo signals
Authors: Farmer W. Todd , Altick Amy L. , Nural Hikmet Feyza , Dugan James P. , Kidd Thomas , Charron Frédéric , Mastick Grant S.
Published: October 2008

Longitudinal axons transmit all signals between the brain and spinal cord. Their axon tracts through the brain stem are established by a simple set of pioneer axons with precise trajectories parallel to the floor plate. To identify longitudinal guidance mechanisms in vivo, the overall role of floor plate tissue and the specific roles of Slit/Robo signals were tested. Ectopic induction or genetic deletion of the floor plate diverted longitudinal axons into abnormal trajectories. The expression patterns of the diffusible cues of the Slit family were altered in the floor plate experiments, suggesting their involvement in longitudinal guidance. Genetic tests of Slit1 and Slit2, and the Slit receptors Robo1 and Robo2 were carried out in mutant mice. Slit1;Slit2 double mutants had severe longitudinal errors,particularly for ventral axons, including midline crossing and wandering longitudinal trajectories. Robo1 and Robo2 were largely genetically redundant, and neither appeared to specify specific tract positions. However, combined Robo1 and Robo2 mutations strongly disrupted each pioneer tract. Thus, pioneer axons depend on long-range floor plate cues, with Slit/Robo signaling required for precise longitudinal trajectories.
Oscillatory models of vibro-impact type for essentially non-linear systems
Authors: Manevitch L I , Gendelman O V
Published: October 2008

This paper reviews recent developments related to oscillatory systems, their impact on and relationship to the cases of smooth, essentially anharmonic (non-linearizable) potentials, and vice versa. Special methods of treatment that allow the response regimes in dynamic vibro-impact systems to be computed have been discussed. Mathematical models that approximate purely elastic as well as inelastic impact, with the help of smooth functions, are presented and illustrated by specific examples. The use of ideas based on non-smooth time transforms to treat essentially non-linear systems with smooth potentials has also been discussed. Special attention has been paid to uncommon applications of vibro-impact models.
Vibro-impact attachments as shock absorbers
Authors: Karayannis I , Vakakis A F , Georgiades F
Published: October 2008

The use of vibro-impact (VI) attachments as shock absorbers is studied. By considering different configurations of primary linear oscillators with VI attachments, the capacity of these attachments to passively absorb and dissipate significant portions of shock energy applied to the primary systems is investigated. Parametric studies are performed to determine the dependence of energy dissipation by the VI attachment in terms of its parameters. Moreover, non-linear shock spectra are used to demonstrate that appropriately designed VI attachments can significantly reduce the maximum levels of vibration of primary systems over wide frequency ranges. This is in contrast to the classical linear vibration absorber, whose action is narrowband. In addition, it is shown that VI attachments can significantly reduce or even completely eliminate resonances appearing in the linear shock spectra, thus providing strong, robust, and broadband shock protection to the primary structures to which they are attached.
Do the bulk solitary strain waves decay?
Authors: Samsonov A M , Dreiden G V , Semenova I V
Published: October 2008

Non-linearly elastic materials may provide generation of strain solitons, even under short-run and reversible (elastic) loading. Theoretical and experimental studies have been performed to prove the existence of long bulk strain solitary waves produced by a laser-induced shock wave in non-linearly elastic isotropic wave guides. Propagation of the bulk solitary density waves is studied in lengthy (over 0.5 m long) elastic wave guides, which have strong dispersion and are made of polymers with remarkable decay of any of the linear or shock waves at short distances. New experiments in lengthy bars confirm that the bulk solitons do not reveal any considerable decay and shape transformation, while linear or shock waves disappear at much shorter distance completely. Decrement values are estimated first for elastic non-linear strain waves decay in polymeric bars.