bluuebunny/crossref_metadata_2025_split huggingface dataset:
The implementation and perception of an OSCE
Authors: Jeppe‐Jensen D. , Larsen T. 
Published: December 2010

The purpose of the present study was to introduce an objective structured clinical examination (OSCE) for educational purposes at a dental school with a rather traditional curriculum in order to encourage reflective thinking in the students. Sixty‐eight third year students in pairs participated in an interdisciplinary OSCE in cariology and microbiology. All stations were based upon one patient testing knowledge, clinical reasoning, verbal communication and practical procedures. At each station, immediate verbal feedback was given to the students by a teacher on the basis of pre‐defined criteria. Further written marks (individual and group averages) were given to the students the following week. After the OSCE, the students and the teachers answered a questionnaire about the OSCE. For practical reasons, the OSCE had to be performed over 3 days and most of the stations to be run by several teachers. The average results obtained by each group did not seem to improve during the week. About half of the students stated not to have discussed the questions with others. There was no apparent systematic variation in the marking of the individual teachers over time. Neither were there major differences between different teachers at the same station, though one teacher marked somewhat lower. Both students and teachers found the OSCE well organised and the questions highly relevant providing an educational benefit. Students as well as teachers perceived the OSCE as a very useful method of clinical assessment, and the vast majority found that OSCEs could also replace parts of the traditional written exams. In conclusion, the OSCE was positively received by students as well as teachers and is recommended for implementation in the curriculum for educational purposes as well as assessment.
Moral education for beginners
Authors: Wilson John 
Published: December 2010

ABSTRACTThis article examines the issue of moral education and especially the role moral educators should take in schools. It critiques a number of well‐known positions, principally those of absolutism, the specification of content and relativism. The author suggests that, though the debate is an immensely difficult one, it is possible to suggest that what we should in fact be doing is giving children in school those attitudes, dispositions, abilities, concepts, skills and other qualities which constitute a good performer in the area of morality. He concludes by providing a list of demonstrably relevant features of this enterprise.
A recipe for success? Localized implementation of a (flexible) National Curriculum
Authors: Cowley Trudy , Williamson John 
Published: December 2010

ABSTRACTNational Curriculum frameworks are now in place in both England and Wales and Australia. Those in England and Wales are seen as prescriptive and rigid, whereas those in Australia are more flexible. Based on case study research as part of the OECD's Innovations in Science, Maths and Technology Education Project, the authors found that the Australian model of national frameworks with localized interpretation and implementation has worked well. Even though Ministers of Education might equate curriculum with content, the authors found that teachers had a much broader view of curriculum and saw it not only as content, but also as including professional development, pedagogy and student‐teacher relationships. Consequently, as a result of adapting the National Curriculum to suit the local context of the school, teachers were changing their pedagogical practices. The data indicate that overprescription with national curricula at the system level should not be attempted and, instead, a more flexible implementation at the local level will result in continuity in curriculum across states, systems, schools and grades, but with a contextualized focus.
A longitudinal study of the effects of implementing a National Curriculum project upon classroom processes
Authors: Hacker R. G. , Rowe M. J. 
Published: December 2010

ABSTRACTThe National Curriculum in the UK is the archetype of centre‐periphery curriculum reform. This article examines whether it has succeeded with particular reference to science. It concludes that changes in classroom behaviours are the opposite of those which might have been anticipated by the curriculum developers. Three possible explanations are suggested: evaluations of teacher effectiveness were too frequent; there have been reduced levels of funding for schools; and an overloaded mandatory curriculum was resulting in a situation where there was a need to cover more curriculum content than had been covered previously. The changes in classroom processes reported in the article, therefore, can hardly be regarded as indicative of the successful implementation of the National Curriculum, though it is possible that they reflect a reaction to moving from a familiar to an unfamiliar situation.
Identifying cancer driver genes in tumor genome sequencing studies
Authors: Youn Ahrim , Simon Richard 
Published: December 2010

AbstractMotivation: Major tumor sequencing projects have been conducted in the past few years to identify genes that contain ‘driver’ somatic mutations in tumor samples. These genes have been defined as those for which the non-silent mutation rate is significantly greater than a background mutation rate estimated from silent mutations. Several methods have been used for estimating the background mutation rate.Results: We propose a new method for identifying cancer driver genes, which we believe provides improved accuracy. The new method accounts for the functional impact of mutations on proteins, variation in background mutation rate among tumors and the redundancy of the genetic code. We reanalyzed sequence data for 623 candidate genes in 188 non-small cell lung tumors using the new method. We found several important genes like PTEN, which were not deemed significant by the previous method. At the same time, we determined that some genes previously reported as drivers were not significant by the new analysis because mutations in these genes occurred mainly in tumors with large background mutation rates.Availability: The software is available at: http://linus.nci.nih.gov/Data/YounA/software.zipContact: rsimon@mail.nih.govSupplementary information: Supplementary data are available at Bioinformatics online.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping
Authors: Lou Shao-Ke , Ni Bing , Lo Leung-Yau , Tsui Stephen Kwok-Wing , Chan Ting-Fung , Leung Kwong-Sak 
Published: December 2010

Abstract
Summary: Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature.
Availability and Implementation: The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.
Contact: tf.chan@cuhk.edu.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
SAIL—a software system for sample and phenotype availability across biobanks and cohorts
Authors: Gostev Mikhail , Fernandez-Banet Julio , Rung Johan , Dietrich Joern , Prokopenko Inga , Ripatti Samuli , McCarthy Mark I. , Brazma Alvis , Krestyaninova Maria 
Published: December 2010

Abstract
Summary: The Sample avAILability system—SAIL—is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables.
Availability: SAIL is available under Aferro-GPL open source license: https://github.com/sail.
Contact: gostev@ebi.ac.uk, support@simbioms.org
Supplementary information: Supplementary data are available at Bioinformatics online and from http://www.simbioms.org.
DROP: an SVM domain linker predictor trained with optimal features selected by random forest
Authors: Ebina Teppei , Toh Hiroyuki , Kuroda Yutaka 
Published: December 2010

Abstract
Motivation: Biologically important proteins are often large, multidomain proteins, which are difficult to characterize by high-throughput experimental methods. Efficient domain/boundary predictions are thus increasingly required in diverse area of proteomics research for computationally dissecting proteins into readily analyzable domains.
Results: We constructed a support vector machine (SVM)-based domain linker predictor, DROP (Domain linker pRediction using OPtimal features), which was trained with 25 optimal features. The optimal combination of features was identified from a set of 3000 features using a random forest algorithm complemented with a stepwise feature selection. DROP demonstrated a prediction sensitivity and precision of 41.3 and 49.4%, respectively. These values were over 19.9% higher than those of control SVM predictors trained with non-optimized features, strongly suggesting the efficiency of our feature selection method. In addition, the mean NDO-Score of DROP for predicting novel domains in seven CASP8 FM multidomain proteins was 0.760, which was higher than any of the 12 published CASP8 DP servers. Overall, these results indicate that the SVM prediction of domain linkers can be improved by identifying optimal features that best distinguish linker from non-linker regions.
Availability: DROP is available at http://tuat.ac.jp/~domserv/DROP.html
Contacts: toh-hiroyuki@aist.go.jp; ykuroda@cc.tuat.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees
Authors: Ta Hung Xuan , Koskinen Patrik , Holm Liisa 
Published: December 2010

Abstract
Motivation: Functional linkages implicate pairwise relationships between proteins that work together to implement biological tasks. During evolution, functionally linked proteins are likely to be preserved or eliminated across a range of genomes in a correlated fashion. Based on this hypothesis, phylogenetic profiling-based approaches try to detect pairs of protein families that show similar evolutionary patterns. Traditionally, the evolutionary pattern of a protein is encoded by either a binary profile of presence and absence of this protein across species or an occurrence profile that indicates the distribution of copies of this protein across species.
Results: In our study, we characterize each protein by its enhanced phylogenetic tree, a novel graphical model of the evolution of a protein family with explicitly marked by speciation and duplication events. By topological comparison between enhanced phylogenetic trees, we are able to detect the functionally associated protein pairs. Because the enhanced phylogenetic trees contain more evolutionary information of proteins, our method shows greater performance and discovers functional linkages among proteins more reliably compared with the conventional approaches.
Contact: xuanhung.ta@helsinki.fi; liisa.holm@helsinki.fi
Sumplementary information: Supplementary data are available at Bioinformatics online.
Adjustment for local ancestry in genetic association analysis of admixed populations
Authors: Wang Xuexia , Zhu Xiaofeng , Qin Huaizhen , Cooper Richard S. , Ewens Warren J. , Li Chun , Li Mingyao 
Published: December 2010

Abstract
Motivation: Admixed populations offer a unique opportunity for mapping diseases that have large disease allele frequency differences between ancestral populations. However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus.
Methods and results: We show that local ancestry at a test single nucleotide polymorphism (SNP) may confound with the association signal and ignoring it can lead to spurious association. We demonstrate theoretically that adjustment for local ancestry at the test SNP is sufficient to remove the spurious association regardless of the mechanism of population stratification, whether due to local or global ancestry differences among study subjects; however, global ancestry adjustment procedures may not be effective. We further develop two novel association tests that adjust for local ancestry. Our first test is based on a conditional likelihood framework which models the distribution of the test SNP given disease status and flanking marker genotypes. A key advantage of this test lies in its ability to incorporate different directions of association in the ancestral populations. Our second test, which is computationally simpler, is based on logistic regression, with adjustment for local ancestry proportion. We conducted extensive simulations and found that the Type I error rates of our tests are under control; however, the global adjustment procedures yielded inflated Type I error rates when stratification is due to local ancestry difference.
Contact: mingyao@upenn.edu; chun.li@vanderbilt.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
Daptomycin Nonsusceptible Enterococci: An Emerging Challenge for Clinicians
Authors: Kelesidis Theodoros , Humphries Romney , Uslan Daniel Z. , Pegues David A. 
Published: December 2010

Abstract
Daptomycin is the only antibiotic with in vitro bactericidal activity against vancomycin-resistant Enterococcus (VRE) that is approved by the Food and Drug Administration (FDA). Data on the potential emergence of daptomycin nonsusceptibility among enterococci remain limited. We systematically reviewed the published literature for reports of isolates of enterococci that were daptomycin nonsusceptible and assessed the clinical significance and outcome of therapy. Based on susceptibility breakpoints approved by the Clinical Laboratory Standards Institute (CLSI), daptomycin has in vitro activity against &gt;90% of enterococcal isolates. Less than 2% of enterococcal isolates were daptomycin nonsusceptible, with minimum inhibitory concentrations (MICs) &gt;4 μg/mL. The prevalence of nonsusceptibility of VRE isolates to daptomycin may be overestimated due to the spread of clonally related isolates in health care settings. Clinicians should be aware of the possibility of the emergence of daptomycin nonsusceptibility and should closely monitor daptomycin MICs of enterococci isolated during treatment.
VOLTAIRE, MARIE-ANTOINETTE, AND THE POLITICS OF
GALANTERIE
Authors: Wynn Thomas 
Published: December 2010

Abstract

In its glorification of the established order,
galanterie
is an aesthetic and practice that lends itself to expressions of fealty. Following Alain Viala's recent research on the subject, this article reconsiders Voltaire's final commission for the French court in the light of the politics of
galanterie. L'Hôte et l'hôtesse
may appear to be a minor frivolity, but an analysis of its political context reveals its importance as a means by which Voltaire attempted to secure royal protection in the wake of Turgot's fall from power in May 1776. The play was intended to contribute to the comte de Provence's
fête galante
for Marie-Antoinette at the château de Brunoy in October of that year. A close reading of Voltaire's proposed texts, the correspondence, and of contemporary accounts of the
fête
allows the received account of the play's production to be challenged. This article reveals Voltaire's attempts to create a suitably
galant
celebration for the queen, in whom he saw a defence against his enemies, and offers a new account for his final failure at the politics of
galanterie
.
Modelling the time-evolution of phytoplankton size spectra from satellite remote sensing
Authors: Roy Shovonlal , Platt Trevor , Sathyendranath Shubha 
Published: December 2010

Abstract
Roy, S., Platt, T., and Sathyendranath, S. 2011. Modelling the time-evolution of phytoplankton size spectra from satellite remote sensing. – ICES Journal of Marine Science, 68: 719–728. A dynamic size-structured model is developed for phytoplankton and nutrients in the oceanic mixed layer and applied to extract phytoplankton biomass at discrete size fractions from remotely sensed, ocean-colour data. General relationships between cell size and biophysical processes (such as sinking, grazing, and primary production) of phytoplankton were included in the model through a bottom–up approach. Time-dependent, mixed-layer depth was used as a forcing variable, and a sequential data-assimilation scheme was implemented to derive model trajectories. From a given time-series, the method produces estimates of size-structured biomass at every observation, so estimates seasonal succession of individual phytoplankton size, derived here from remote sensing for the first time. From these estimates, normalized phytoplankton biomass size spectra over a period of 9 years were calculated for one location in the North Atlantic. Further analysis demonstrated that strong relationships exist between the seasonal trends of the estimated size spectra and the mixed-layer depth, nutrient biomass, and total chlorophyll. The results contain useful information on the time-dependent biomass flux in the pelagic ecosystem.
Protein Kinase A–dependent Spinal α-Amino-3-hydroxy-5-methyl-4-isoxazoleproprionate–receptor Trafficking Mediates Capsaicin-induced Colon-Urethra Cross-organ Reflex Sensitization
Authors: Peng Hsien-Yu , Chang Chao-Hsiang , Tsai Shin-Jei , Lai Cheng-Yuan , Tung Kwong-Chung , Wu Hsi-Chin , Lin Tzer-Bin 
Published: December 2010

Background
Intracellular redistribution of α-amino-3-hydroxy-5-methyl-4-isoxazoleproprionate receptors (AMPARs) is known to be induced by natural painful stimulation. We tested the hypothesis that that protein kinase A (PKA)-dependent AMPAR trafficking underlies the development of N-methyl-d-aspartate receptor-mediated cross-organ sensitization in vivo.

Methods
We recorded urethra reflex activity and analyzed immunoblotting of lumbosacral (L6-S2) dorsal horn (DH) tissue obtained from animal preparations after intrathecal 8-bromo-cyclic adenosine monophosphate injection or intracolonic instillation with 8-methyl-N-vanillyl-trans-6-nonenamide (capsaicin).

Results
Intrathecal 8-bromo-cyclic adenosine monophosphate (300 μM, 10 μl) induced reflex potentiation (81.85 ± 22.21 spikes/stimulation) and increased the number of AMPAR Glu receptor 1 subunits in the membrane fraction of DH (1.8-fold increase vs. control). This process was prevented by pretreatment with the PKA inhibitor N-[2- ((p-bromocinnamyl)amino)ethyl]-5-isoquinolinesulfonamide(10 μM, 10 μl, 2.7 ± 0.8 [mean ± SE] spikes/stimulation) and human thyroid A kinase-anchoring protein (10 μM, 10 μl, 11.5 ± 4.8 spikes/stimulation), an inhibitor of PKA and PKA-A kinase-anchoring protein interactions. Intracolonic capsaicin instillation sensitized the urethra reflex (137.2 ± 62.4 spikes/stimulation) and, relative to control, simultaneously provoked an increase (2.9-fold) in the membrane fraction and a decrease (0.9-fold) in the cytosolic fraction of Glu receptor 1 subunits in DH. Inhibition of PKA activity and disruption of PKA-A kinase-anchoring protein interaction in the DH (2.0 ± 0.6 and 16.7 ± 2.8 spikes/stimulation, respectively) are sufficient to prevent capsaicin-dependent reflex sensitization and AMPAR trafficking in the membrane fraction (0.6- and 0.5-fold increase capsaicin).

Conclusion
Delivery of AMPAR-containing Glu receptor 1 subunits to the membranes of lumbosacral DH neurons through a PKA-dependent pathway contributes to noxious stimulation-induced synaptic strengthening, which plays roles in colon-urethra reflex sensitization.
Continuous Measurement of Blood Glucose
Authors: Skjaervold Nils K. , Solligård Erik , Hjelme Dag R. , Aadahl Petter 
Published: December 2010

Background
Tight blood glucose control is used extensively in perioperative and critically ill patients. Several studies, however, have shown contradictory effects on patient outcomes. A major problem of these studies has been inadequate control of the prime variable, blood glucose. This paper describes the validation of a new intravascular continuous blood glucose sensor.

Methods
The glucose sensor was placed in the superior caval vein of seven anesthetized pigs. Sensor readings were compared with arterial blood gas readings. Fluctuations in blood glucose were created using intravenous glucose and insulin. A total of 807 paired sensor and blood gas readings were obtained.

Results
The sensor was tested with a range of blood glucose values (0.63-15.75 mM [mean bias, 0.0131 mM]). Analysis using Bland-Altman plots yielded 95% limits of agreement at -0.908 and 0.934 mM. There were 121 paired measurements with a mean value below 2.2 mM, yielding 95% limits of agreement at -0.553 and 0.466 mM.

Conclusions
The performance of the sensor was in agreement with blood gas measurements in a wide range of glucose values. For the clinician, it is noteworthy that performance was equally good in the hypoglycemic area.