bluuebunny/crossref_metadata_2025 huggingface dataset:
From the myth of Prometheus to strategic resilience: two cognitive paradigms linking risk and innovation
Authors: Marshall Alasdair , Ojiako Udechukwu
Published: December 2010

We argue that cognition linking risk to innovation is influenced by two distinct cognitive paradigms which have deep roots in personality and culture and are closely bound up with political identity. We differentiate between a paradigm of Promethean conservatism where innovation is perceived as threatening, and a paradigm of ‘Strategic Resilience’, where the status quo is perceived as threatening and innovation is perceived to reduce this threat. We find an evidence base for these paradigms in the personality psychology literature, which shows a strong tendency for psychometric measures of risk and innovation to correlate positively with each other and negatively with measures of conservatism and authoritarianism. We develop four theoretical elaborations from this greatly underutilised evidence base: (1) we seem to possess powerful ‘implicit personality theories’ (IPTs) which conflate the risk taker with the innovator; (2) these IPTs lead us to evaluate risk‐taking innovation either positively or negatively; (3) these evaluations also manifest the positions we adopt, as we undertake identity work, along the rich and complex personological and cultural continuum that contrasts risk‐averse conservatism with liberal radicalism; and (4) this highly political self‐positioning carries multiple implications for how we identify and evaluate risk within the context of organisational innovation.
Moral education for beginners
Authors: Wilson John
Published: December 2010

This 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

National 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

The 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.
A three-dimensional sharp interface model for self-consistent keyhole and weld pool dynamics in deep penetration laser welding
Authors: Pang Shengyong , Chen Liliang , Zhou Jianxin , Yin Yajun , Chen Tao
Published: December 2010

A three-dimensional sharp interface model is proposed to investigate the self-consistent keyhole and weld pool dynamics in deep penetration laser welding. The coupling of three-dimensional heat transfer, fluid flow and keyhole free surface evolutions in the welding process is simulated. It is theoretically confirmed that under certain low heat input welding conditions deep penetration laser welding with a collapsing free keyhole could be obtained and the flow directions near the keyhole wall are upwards and approximately parallel to the keyhole wall. However, significantly different weld pool dynamics in a welding process with an unstable keyhole are numerically found. Many flow patterns in the welding process with an unstable keyhole, verified by x-ray transmission experiments, were successfully simulated and analysed. Periodical keyhole collapsing and bubble formation processes are also successfully simulated and believed to be in good agreement with experiments. The mechanisms of keyhole instability are found to be closely associated with the behaviour of humps on the keyhole wall, and it is found that the welding speed and surface tension are closely related to the formation of humps on the keyhole wall. It is also shown that the weld pool dynamics in laser welding with an unstable keyhole are closely associated with the transient keyhole instability and therefore modelling keyhole and weld pool in a self-consistent way is significant to understand the physics of laser welding.
Thickness-dependent fracture behaviour of flexible ZnO : Al thin films
Authors: Mohanty Bhaskar Chandra , Choi Hong Rak , Choi Yong Muk , Cho Yong Soo
Published: December 2010

The effects of thickness on flexibility and crack initiation in ZnO : Al thin films sputter-deposited on polyethersulfone substrates have been investigated. With an increase in thickness, root-mean-square roughness and average crystallite size increase linearly. It is found that the higher the thickness, the lower is the strain required to initiate cracks in the film. The thinnest film (∼240 nm) exhibits a crack-initiating critical strain of 0.96% and a saturated crack density of 0.10 µm−1. A critical energy release rate of 68.5 J m−2 and a mode I fracture toughness of 3.2 MPa m0.5 are estimated for the films. These parameters are found to exhibit a linear dependence on film thickness.
Influence of template type and buffer strain on structural properties of GaN multilayer quantum wells grown by PAMBE, an x-ray study
Authors: Kladko V P , Kuchuk A V , Safryuk N V , Machulin V F , Lytvyn P M , Raicheva V G , Belyaev A E , Mazur Yu I , Jr E A DeCuir , Ware M E , Manasreh M O , Salamo G J
Published: December 2010

The influence of template type and residual strain of the buffer layer on the structural properties of GaN/AlN superlattices (SLs) was studied using high resolution x-ray diffraction. Using sapphire substrates, an effective thinning of the GaN quantum wells and the corresponding thickening of the AlN barriers were observed in SL structures grown on thin, strained AlN templates as compared with SL structures grown on thick, relaxed GaN templates. Moreover, a bimodal strain relaxation of SL structures in dependence of template type was observed. The SLs grown on AlN templates relax predominantly by the formation of misfit dislocations, while the SLs grown on GaN templates relax predominantly by cracking of the layers. We explain these effects by the influence of residual strain in the buffer/template systems used for the growth processes of SL layers. A correlation is made between the strain state of the system and the cracking processes, the dislocation density, the radius of curvature and the layer thickness.
Recruitment of dynein to late endosomes and lysosomes through light intermediate chains
Authors: Tan Serena C. , Scherer Julian , Vallee Richard B.
Published: December 2010

Cytoplasmic dynein is involved in a wide range of cellular processes, but how it is regulated and how it recognizes an extremely wide range of cargo are incompletely understood. The dynein light intermediate chains, LIC1 and LIC2 (DYNC1LI1 and DYNC1LI2, respectively), have been implicated in cargo binding, but their full range of functions is unknown. Using LIC isoform-specific antibodies, we report the first characterization of their subcellular distribution and identify a specific association with elements of the late endocytic pathway, but not other vesicular compartments. LIC1 and LIC2 RNA interference (RNAi) each specifically disrupts the distribution of lysosomes and late endosomes. Stimulation of dynein-mediated late-endosomal transport by the Rab7-interacting lysosomal protein (RILP) is reversed by LIC1 RNAi, which displaces dynein, but not dynactin, from these structures. Conversely, expression of ΔN-RILP or the dynactin subunit dynamitin each fails to displace dynein, but not dynactin. Thus, using a variety of complementary approaches, our results indicate a novel specific role for the LICs in dynein recruitment to components of the late endocytic pathway.
Huntingtin coordinates the dynein-mediated dynamic positioning of endosomes and lysosomes
Authors: Caviston Juliane P. , Zajac Allison L. , Tokito Mariko , Holzbaur Erika L.F.
Published: December 2010

Huntingtin (Htt) is a membrane-associated scaffolding protein that interacts with microtubule motors as well as actin-associated adaptor molecules. We examined a role for Htt in the dynein-mediated intracellular trafficking of endosomes and lysosomes. In HeLa cells depleted of either Htt or dynein, early, recycling, and late endosomes (LE)/lysosomes all become dispersed. Despite altered organelle localization, kinetic assays indicate only minor defects in intracellular trafficking. Expression of full-length Htt is required to restore organelle localization in Htt-depleted cells, supporting a role for Htt as a scaffold that promotes functional interactions along its length. In dynein-depleted cells, LE/lysosomes accumulate in tight patches near the cortex, apparently enmeshed by cortactin-positive actin filaments; Latrunculin B-treatment disperses these patches. Peripheral LE/lysosomes in dynein-depleted cells no longer colocalize with microtubules. Htt may be required for this off-loading, as the loss of microtubule association is not seen in Htt-depleted cells or in cells depleted of both dynein and Htt. Inhibition of kinesin-1 relocalizes peripheral LE/lysosomes induced by Htt depletion but not by dynein depletion, consistent with their detachment from microtubules upon dynein knockdown. Together, these data support a model of Htt as a facilitator of dynein-mediated trafficking that may regulate the cytoskeletal association of dynamic organelles.
Role of Pax3 acetylation in the regulation ofHes1andNeurog2
Authors: Ichi Shunsuke , Boshnjaku Vanda , Shen Yueh-Wei , Mania-Farnell Barbara , Ahlgren Sara , Sapru Sidanth , Mansukhani Nikhita , McLone David G. , Tomita Tadanori , Mayanil C.S.K.
Published: December 2010

Pax3 plays a role in regulating Hes1 and Neurog2 activity and thereby stem cell maintenance and neurogenesis. A mechanism for Pax3 regulation of these two opposing events, during caudal neural tube development, is examined in this study. Pax3 acetylation on C-terminal lysine residues K437 and K475 may be critical for proper regulation of Hes1 and Neurog2. Removal of these lysine residues increased Hes1 but decreased Neurog2 promoter activity. SIRT1 deacetylase may be a key component in regulating Pax3 acetylation. Chromatin immunoprecipitation assays showed that SIRT1 is associated with Hes1 and Neurog2 promoters during murine embryonic caudal neural tube development at E9.5, but not at E12.5. Overexpression of SIRT1 decreased Pax3 acetylation, Neurog2 and Brn3a positive staining. Conversely, siRNA-mediated silencing of SIRT1 increased these factors. These studies suggest that Pax3 acetylation results in decreased Hes1 and increased Neurog2 activity, thereby promoting sensory neuron differentiation.
Identifying cancer driver genes in tumor genome sequencing studies
Authors: Youn Ahrim , Simon Richard
Published: December 2010

Motivation: 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.zip

Contact:  rsimon@mail.nih.gov

Supplementary 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

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

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

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

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

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

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 >90% of enterococcal isolates. Less than 2% of enterococcal isolates were daptomycin nonsusceptible, with minimum inhibitory concentrations (MICs) >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

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

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.
p38 Mitogen–activated Protein Kinase Activation by Nerve Growth Factor in Primary Sensory Neurons Upregulates μ-Opioid Receptors to Enhance Opioid Responsiveness Toward Better Pain Control
Authors: Yamdeu Reine-Solange , Shaqura Mohammed , Mousa Shaaban A. , Schäfer Michael , Droese Jana
Published: December 2010

Background

Sensory neuron opioid receptors are targets for spinal, epidural, and peripheral opioid application. Although local nerve growth factor (NGF) has been identified as a mediator of sensory neuron μ-opioid receptor (MOR) up-regulation, the signaling pathways involved have not been yet identified.

Methods

Wistar rats were treated with intraplantar vehicle, Freund's complete adjuvant, NGF, NGF plus intrathecal p38 mitogen-activated protein kinase (MAPK) inhibitors, or NGF plus extracellular signal-regulated kinase-1/2 MAPK inhibitors. After 4 days of treatment, paw pressure thresholds of an intraplantar full (fentanyl) or partial (buprenorphine) opioid agonist were determined by algesiometry. Tissue samples from rat dorsal root ganglia were subjected to radiolabeled ligand binding, Western blot analysis, and confocal immunofluorescence.

Results

Exogenous and endogenous NGF resulting from Freund's complete adjuvant inflammation produced significant potentiation and enhanced efficacy in fentanyl- and buprenorphine-induced dose-dependent antinociception, respectively. Furthermore, in the ipsilateral dorsal root ganglia, NGF produced a significant increase in MOR binding sites, proteins, and immunoreactive neurons. In parallel, phosphorylated p38-MAPK protein, the number of phosphorylated p38-MAPK immunoreactive neurons expressing MOR in dorsal root ganglia, and the peripherally directed axonal transport of MOR significantly increased. Finally, NGF-induced effects occurring in dorsal root ganglia, on axonal transport, and on the potentiation or enhanced efficacy of opioid antinociception were abrogated by inhibition of p38, but not extracellular signal-regulated kinase-1/2, MAPK.

Conclusions

Local NGF through activation of the p38-MAPK pathway leads to adaptive changes in sensory neuron MOR toward enhanced susceptibility to local opioids. This effect may act as a counter-regulatory response to p38-MAPK-induced pain (e.g., inflammatory pain) to facilitate opioid-mediated antinociception.
Ochrobactrum daejeonense sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant
Authors: Woo Sung-Geun , Ten Leonid N. , Park Joonhong , Lee Myungjin
Published: December 2010

A Gram-reaction-negative, non-spore-forming, rod-shaped, aerobic bacterial strain, designated MJ11T, was isolated from sludge of a leachate treatment plant in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ11T belonged to the family Brucellaceae, class Alphaproteobacteria, and was most closely related to Ochrobactrum ciceri Ca-34T (97.9 % sequence similarity) and Ochrobactrum pituitosum CCUG 50899T (96.4 %). Comparative sequence analyses of the additional phylogenetic marker genes dnaK, groEL and gyrB confirmed the affiliation of strain MJ11T to the genus Ochrobactrum. The G+C content of the genomic DNA of strain MJ11T was 59.3 mol%. The detection of a quinone system with ubiquinone Q-10 as the predominant respiratory lipoquinone, a fatty acid profile with C18 : 1ω7c (62.6 %) and C19 : 0 cyclo ω8c (14.2 %) as the major components, a polar lipid profile with phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and unknown aminolipids AL1 and AL2 as major polar lipids and spermidine and putrescine as the predominant polyamines also supported the affiliation of strain MJ11T to the genus Ochrobactrum. The DNA–DNA relatedness between strain MJ11T and Ochrobactrum ciceri DSM 22292T was 29±7 %, clearly showing that the isolate constitutes a new genospecies. Strain MJ11T could be clearly differentiated from its closest neighbours on the basis of its phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ11T represents a novel species of the genus Ochrobactrum, for which the name Ochrobactrum daejeonense sp. nov. is proposed. The type strain is MJ11T ( = KCTC 22458T  = JCM 16234T).
Halobellus clavatus gen. nov., sp. nov. and Halorientalis regularis gen. nov., sp. nov., two new members of the family Halobacteriaceae
Authors: Cui Heng-Lin , Yang Xin , Gao Xia , Xu Xue-Wei
Published: December 2010

Four halophilic archaeal strains, designated TNN18T, TBN12, TNN28T and TBN19, were isolated from brines sampled from two artificial marine solar salterns in eastern China. Strains TNN18T and TNN28T were isolated from the Tainan marine solar saltern, whereas strains TBN12 and TBN19 were from the Taibei marine solar saltern. Colonies of the four strains were red-pigmented and their cells were pleomorphic, motile, Gram-reaction-negative rods. Strains TNN18T and TBN12 were able to grow at 25–50 °C (optimum 37 °C), in 10–30 % (w/v) NaCl (optimum 15 %), with 0–1.0 M MgCl2 (optimum 0.05 M) and at pH 5.5–9.0 (optimum pH 7.0–7.5), while strains TNN28T and TBN19 were able to grow at 20–50 °C (optimum 37 °C), in 15-30 % (w/v) NaCl (optimum 18–20 %), in 0.005–1.0 M MgCl2 (optimum 0.01–0.3 M) and at pH 6.0–9.0 (optimum pH 7.0–7.5). Cells of these strains lyse in distilled water; minimal NaCl concentrations to prevent cell-lysis are 10 % (w/v) for strains TNN18T and TBN12 and 12 % (w/v) for strains TNN28T and TBN19. The major polar lipids of strains TNN18T and TBN12 were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS) and one major glycolipid (GL1), which was chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). Minor amounts of other lipids (GL0, GL2, GL3 and GL4) were also detectable. The polar lipid profiles of strains TNN28T and TBN19 contained PG, PGP-Me, GL1, which was chromatographically identical to S-DGD-1, and three to four minor unidentified glycolipids (GL2–GL5). Phylogenetic analyses revealed that strains TNN18T and TBN12 formed a distinct clade with strains of the closest related species, Haloquadratum walsbyi (91.5–91.8 % 16S rRNA gene sequence similarity) and strains TNN28T and TBN19 formed a distinct clade with strains of the species Halosimplex carlsbadense (89.9–93.3 % similarity) and two members of the genus Halorhabdus (92.5–93.3 % similarity). The DNA G+C contents of strains TNN18T, TBN12, TNN28T and TBN19 were 61.5, 62.4, 61.9 and 61.5 mol%, respectively. DNA–DNA hybridization values between strains TNN18T and TBN12, and strains TNN28T and TBN19 were 82.9 % and 88.2 %, respectively. The phenotypic, chemotaxonomic and phylogenetic properties suggest that the four strains represent two novel species of two new genera within the family Halobacteriaceae, for which the names Halobellus clavatus gen. nov., sp. nov. (type strain TNN18T  = CGMCC 1.10118T  = JCM 16424T) and Halorientalis regularis gen. nov., sp. nov. (type strain TNN28T  = CGMCC 1.10123T  = JCM 16425T) are proposed.
Fervidobacterium riparium sp. nov., a thermophilic anaerobic cellulolytic bacterium isolated from a hot spring
Authors: Podosokorskaya Olga A. , Merkel Alexandr Yu. , Kolganova Tatyana V. , Chernyh Nikolai A. , Miroshnichenko Margarita L. , Bonch-Osmolovskaya Elizaveta A. , Kublanov Ilya V.
Published: December 2010

A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain 1445tT, was isolated from a hot spring on Kunashir Island (Kuril Islands, Russia). Cells were motile rods (0.4–0.5×1.0–3.0 µm). The temperature range for growth at pH 7.8 was 46–80 °C, with optimum growth at 65 °C. The pH range for growth at 65 °C was pH 5.7–9.0, with optimum growth at pH 7.8. Growth was not observed at or below 40 °C, at or above 84 °C, at or below pH 5.4 or at or above pH 9.5. The isolate degraded a wide range of substrates including starch, cellulose and cellulose derivatives. Elemental sulfur stimulated growth, but sodium sulfate, sulfite and thiosulfate did not. DNA G+C content was 31 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain 1445tTbelonged to the genusFervidobacterium. 16S rRNA gene sequence similarities with strains of other species of the genusFervidobacteriumwere 94.9–98.3 %; the type strain ofFervidobacterium gondwanensewas the closest relative of strain 1445tT. DNA–DNA hybridization of strain 1445tTandF. gondwanenseAB39Trevealed a relatedness value of 20 %. Based on phylogenetic data and physiological properties of the isolate, a novel species, designatedFervidobacterium ripariumsp. nov., is proposed with strain 1445tT( = DSM 21630T = VKM B-2549T) as the type strain.
Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea
Authors: Khelaifia Saber , Fardeau Marie-Laure , Pradel Nathalie , Aussignargues Clément , Garel Marc , Tamburini Christian , Cayol Jean-Luc , Gaudron Sylvie , Gaill Françoise , Ollivier Bernard
Published: December 2010

A novel sulfate-reducing bacterium, designated C1TLV30T, was isolated from wood falls at a depth of 1693 m in the Mediterranean Sea. Cells were motile vibrios (2–4×0.5 µm). Strain C1TLV30T grew at temperatures between 15 and 45 °C (optimum 30 °C) and at pH 5.4–8.6 (optimum 7.3). It required NaCl for growth (optimum at 25 g NaCl l−1) and tolerated up to 80 g NaCl l−1. Strain C1TLV30T used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. The end products from lactate oxidation were acetate, H2S and CO2 in the presence of sulfate as terminal electron acceptor. Besides sulfate, thiosulfate and sulfite were also used as terminal electron acceptors, but not elemental sulfur, fumarate, nitrate or nitrite. Strain C1TLV30T possessed desulfoviridin and was piezophilic, growing optimally at 10 MPa (range 0–30 MPa). The membrane lipid composition of this strain was examined to reveal an increase in fatty acid chain lengths at high hydrostatic pressures. The G+C content of the genomic DNA was 49.6 % and the genome size was estimated at 3.5±0.5 Mb. Phylogenetic analysis of the SSU rRNA gene sequence indicated that strain C1TLV30T was affiliated to the genus Desulfovibrio with Desulfovibrio profundus being its closest phylogenetic relative (similarity of 96.4 %). On the basis of SSU rRNA gene sequence comparisons and physiological characteristics, strain C1TLV30T ( = DSM 21447T  = JCM 1548T) is proposed to be assigned to a novel species of the genus Desulfovibrio, Desulfovibrio piezophilus sp. nov.
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
Authors: Ip Joanna Y. , Schmidt Dominic , Pan Qun , Ramani Arun K. , Fraser Andrew G. , Odom Duncan T. , Blencowe Benjamin J.
Published: December 2010

The rate of RNA polymerase II (Pol II) elongation can influence splice site selection in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing (AS) is not well understood. We performed experiments to perturb Pol II elongation and then globally compared AS patterns with genome-wide Pol II occupancy. RNA binding and RNA processing functions were significantly enriched among the genes with Pol II elongation inhibition-dependent changes in AS. Under conditions that interfere with Pol II elongation, including cell stress, increased Pol II occupancy was detected in the intronic regions flanking the alternative exons in these genes, and these exons generally became more included. A disproportionately high fraction of these exons introduced premature termination codons that elicited nonsense-mediated mRNA decay (NMD), thereby further reducing transcript levels. Our results provide evidence that kinetic coupling between transcription, AS, and NMD affords a rapid mechanism by which cells can respond to changes in growth conditions, including cell stress, to coordinate the levels of RNA processing factors with mRNA levels.
PKA and PKC are required for long-term but not short-term in vivo operant memory in Aplysia
Authors: Michel Maximilian , Green Charity L. , Lyons Lisa C.
Published: December 2010

We investigated the involvement of PKA and PKC signaling in a negatively reinforced operant learning paradigm in Aplysia, learning that food is inedible (LFI). In vivo injection of PKA or PKC inhibitors blocked long-term LFI memory formation. Moreover, a persistent phase of PKA activity, although not PKC activity, was necessary for long-term memory. Surprisingly, neither PKA nor PKC activity was required for associative short-term LFI memory. Additionally, PKA and PKC were not required for the retrieval of short- or long-term memory (STM and LTM, respectively). These studies have identified key differences between the mechanisms underlying nonassociative sensitization, operant reward learning, and LFI memory in Aplysia.
Reactivation of Meristem Activity and Sprout Growth in Potato Tubers Require Both Cytokinin and Gibberellin
Authors: Hartmann Anja , Senning Melanie , Hedden Peter , Sonnewald Uwe , Sonnewald Sophia
Published: December 2010

Reactivation of dormant meristems is of central importance for plant fitness and survival. Due to their large meristem size, potato (Solanum tuberosum) tubers serve as a model system to study the underlying molecular processes. The phytohormones cytokinins (CK) and gibberellins (GA) play important roles in releasing potato tuber dormancy and promoting sprouting, but their mode of action in these processes is still obscure. Here, we established an in vitro assay using excised tuber buds to study the dormancy-releasing capacity of GA and CK and show that application of gibberellic acid (GA3) is sufficient to induce sprouting. In contrast, treatment with 6-benzylaminopurine induced bud break but did not support further sprout growth unless GA3 was administered additionally. Transgenic potato plants expressing Arabidopsis (Arabidopsis thaliana) GA 20-oxidase or GA 2-oxidase to modify endogenous GA levels showed the expected phenotypical changes as well as slight effects on tuber sprouting. The isopentenyltransferase (IPT) from Agrobacterium tumefaciens and the Arabidopsis cytokinin oxidase/dehydrogenase1 (CKX) were exploited to modify the amounts of CK in transgenic potato plants. IPT expression promoted earlier sprouting in vitro. Strikingly, CKX-expressing tubers exhibited a prolonged dormancy period and did not respond to GA3. This supports an essential role of CK in terminating tuber dormancy and indicates that GA is not sufficient to break dormancy in the absence of CK. GA3-treated wild-type and CKX-expressing tuber buds were subjected to a transcriptome analysis that revealed transcriptional changes in several functional groups, including cell wall metabolism, cell cycle, and auxin and ethylene signaling, denoting events associated with the reactivation of dormant meristems.
TheArabidopsisGTL1 Transcription Factor Regulates Water Use Efficiency and Drought Tolerance by Modulating Stomatal Density via Transrepression ofSDD1
Authors: Yoo Chan Yul , Pence Heather E. , Jin Jing Bo , Miura Kenji , Gosney Michael J. , Hasegawa Paul M. , Mickelbart Michael V.
Published: December 2010

A goal of modern agriculture is to improve plant drought tolerance and production per amount of water used, referred to as water use efficiency (WUE). Although stomatal density has been linked to WUE, the causal molecular mechanisms have yet to be determined. Arabidopsis thaliana  GT-2 LIKE 1 (GTL1) loss-of-function mutations result in increased water deficit tolerance and higher integrated WUE by reducing daytime transpiration without a demonstrable reduction in biomass accumulation. gtl1 plants had higher instantaneous WUE that was attributable to ~25% lower transpiration and stomatal conductance but equivalent CO2 assimilation. Lower transpiration was associated with higher STOMATAL DENSITY AND DISTRIBUTION1 (SDD1) expression and an ~25% reduction in abaxial stomatal density. GTL1 expression occurred in abaxial epidermal cells where the protein was localized to the nucleus, and its expression was downregulated by water stress. Chromatin immunoprecipitation analysis indicated that GTL1 interacts with a region of the SDD1 promoter that contains a GT3 box. An electrophoretic mobility shift assay was used to determine that the GT3 box is necessary for the interaction between GTL1 and the SDD1 promoter. These results establish that GTL1 negatively regulates WUE by modulating stomatal density via transrepression of SDD1.
Modelling and optimisation study on the fabrication of nano‐structures using imprint forming process
Authors: Stoyanov Stoyan , Tilford Tim , Amalou Farid , Cargill Scott , Bailey Chris , Desmulliez Marc
Published: December 2010

Purpose

Nano‐imprint forming (NIF) is a manufacturing technology capable of achieving high resolution, low‐cost and high‐throughput fabrication of fine nano‐scale structures and patterns. The purpose of this paper is to use modelling technologies to simulate key process steps associated with the formation of patterns with sub‐micrometer dimensions and use the results to define design rules for optimal imprint forming process.

Design/methodology/approach

The effect of a number of process and pattern‐related parameters on the quality of the fabricated nano‐structures is studied using non‐linear finite element analysis. The deformation process of the formable material during the mould pressing step is modelled using contact analysis with large deformations and temperature dependent hyperelastic material behaviour. Finite element analysis with contact interfaces between the mould and the formable material is utilised to study the formation of mechanical, thermal and friction stresses in the pattern.

Findings

The imprint pressure, temperature and the aspect ratio of grooves which define the pattern have significant effect on the quality of the formed structures. The optimal imprint pressure for the studied PMMA is identified. It is found that the degree of the mould pattern fulfilment as function of the imprint pressure is non‐linear. Critical values for thermal mismatch difference in the CTE between the mould and the substrate causing thermally induced stresses during cooling stage are evaluated. Regions of high stresses in the pattern are also identified.

Originality/value

Design rules for minimising the risk of defects such as cracks and shape imperfections commonly observed in NIF‐fabricated nano‐structures are presented. The modelling approach can be used to provide insights into the optimal imprint process control. This can help to establish further the technology as a viable route for fabrication of nano‐scale structures and patterns.