bluuebunny/crossref_metadata_2025 huggingface dataset:
Precipitation process and rainfall intensity differentiation using Meteosat Second Generation Spinning Enhanced Visible and Infrared Imager data
Authors: Thies Boris , Nauß Thomas , Bendix Jörg
Published: December 2008

A new day and night technique for precipitation process separation and rainfall intensity differentiation using the Meteosat Second Generation Spinning Enhanced Visible and Infrared Imager is proposed. It relies on the conceptual design that convective clouds with higher rainfall intensities are characterized by a larger vertical extension and a higher cloud top. For advective‐stratiform precipitation areas, it is assumed that areas with a higher cloud water path (CWP) and more ice particles in the upper parts are characterized by higher rainfall intensities. First, the rain area is separated into areas of convective and advective‐stratiform precipitation processes. Next, both areas are divided into subareas of differing rainfall intensities. The classification of the convective area relies on information about the cloud top height gained from water vapor‐IR differences and the IR cloud top temperature. The subdivision of the advective‐stratiform area is based on information about the CWP and the particle phase in the upper parts. Suitable combinations of temperature differences (ΔT3.9–10.8, ΔT3.9–7.3, ΔT8.7–10.8, ΔT10.8–12.1) are incorporated to infer information about the CWP during nighttime, while a visible and a near‐IR channel are considered during the daytime. ΔT8.7–10.8 and ΔT10.8–12.1 are particularly included to supply information about the cloud phase. Intensity differentiation is realized by using pixel‐based confidences for each subarea calculated as a function of the respective value combinations of the previously mentioned variables. For the calculation of the confidences, the value combinations are compared with ground‐based radar data. The proposed technique is validated against ground‐based radar data and shows an encouraging performance (Heidke skill score 0.07–0.2 for 15‐min intervals).
Sampling uncertainties in surface radiation budget calculations in RADAGAST
Authors: Settle J. J. , Bharmal N. A. , Robinson G. J. , Slingo A.
Published: December 2008

In the Radiative Atmospheric Divergence Using ARM Mobile Facility GERB and AMMA Stations (RADAGAST) project we calculate the divergence of radiative flux across the atmosphere by comparing fluxes measured at each end of an atmospheric column above Niamey, in the African Sahel region. The combination of broadband flux measurements from geostationary orbit and the deployment for over 12 months of a comprehensive suite of active and passive instrumentation at the surface eliminates a number of sampling issues that could otherwise affect divergence calculations of this sort. However, one sampling issue that challenges the project is the fact that the surface flux data are essentially measurements made at a point, while the top‐of‐atmosphere values are taken over a solid angle that corresponds to an area at the surface of some 2500 km2. Variability of cloud cover and aerosol loading in the atmosphere mean that the downwelling fluxes, even when averaged over a day, will not be an exact match to the area‐averaged value over that larger area, although we might expect that it is an unbiased estimate thereof. The heterogeneity of the surface, for example, fixed variations in albedo, further means that there is a likely systematic difference in the corresponding upwelling fluxes. In this paper we characterize and quantify this spatial sampling problem. We bound the root‐mean‐square error in the downwelling fluxes by exploiting a second set of surface flux measurements from a site that was run in parallel with the main deployment. The differences in the two sets of fluxes lead us to an upper bound to the sampling uncertainty, and their correlation leads to another which is probably optimistic as it requires certain other conditions to be met. For the upwelling fluxes we use data products from a number of satellite instruments to characterize the relevant heterogeneities and so estimate the systematic effects that arise from the flux measurements having to be taken at a single point. The sampling uncertainties vary with the season, being higher during the monsoon period. We find that the sampling errors for the daily average flux are small for the shortwave irradiance, generally less than 5 W m−2, under relatively clear skies, but these increase to about 10 W m−2 during the monsoon. For the upwelling fluxes, again taking daily averages, systematic errors are of order 10 W m−2 as a result of albedo variability. The uncertainty on the longwave component of the surface radiation budget is smaller than that on the shortwave component, in all conditions, but a bias of 4 W m−2 is calculated to exist in the surface leaving longwave flux.
DNA‐PK suppresses a p53‐independent apoptotic response to DNA damage
Authors: Gurley Kay E , Moser Russell , Gu Yansong , Hasty Paul , Kemp Christopher J
Published: December 2008

p53 is required for DNA damage‐induced apoptosis, which is central to its function as a tumour suppressor. Here, we show that the apoptotic defect of p53‐deficient cells is nearly completely rescued by inactivation of any of the three subunits of the DNA repair holoenzyme DNA‐dependent protein kinase (DNA‐PK). Intestinal crypt cells from p53 nullizygous mice were resistant to radiation‐induced apoptosis, whereas apoptosis in DNA‐PKcs/p53, Ku80/p53 and Ku70/p53 double‐null mice was quantitatively equivalent to that seen in wild‐type mice. This p53‐independent apoptotic response was specific to the loss of DNA‐PK, as it was not seen in ligase IV (Lig4)/p53 or ataxia telangiectasia mutated (Atm)/p53 double‐null mice. Furthermore, it was associated with an increase in phospho‐checkpoint kinase 2 (CHK2), and cleaved caspases 3 and 9, the latter indicating engagement of the intrinsic apoptotic pathway. This shows that there are two separate, but equally effective, apoptotic responses to DNA damage: one is p53 dependent and the other, engaged in the absence of DNA‐PK, does not require p53.
A Methodology for the Inclusion of Laboratory Assessment in the Evaluation of Dysphagia
Authors: Mills Russell H. , Ashford John R.
Published: December 2008

Detecting aspiration appears to be a major objective of any assessment for oropharyngeal dysphagia as a precursor to preventing pneumonia development. Convincing evidence supporting this clinical belief remains elusive. To the contrary, other variables of the patient's prevailing health status appear to be much better predictors. The purposes of this article are to discuss dysphagia as it relates to a specific health status model, to describe how specific blood tests are used to examine health status variables, and to provide discussion of the use of laboratory assessments to examine immune system status and infection and their potential relationship with pneumonia.
Concepts in Ventilator Weaning: Challenges for the Patient With Dysphagia
Authors: Dikeman Karen , Kazandjian Marta , Lerner Helene
Published: December 2008

The care of the mechanically ventilated patient has evolved over the past several decades. Individuals who have had tracheostomies and are dependent on ventilators often experience a devastating loss of communication and swallowing function. More and more frequently, speech-language pathologists are called upon to assist in the care of these patients with medically complex conditions as part of a comprehensive interdisciplinary team. When working with patients who are being weaned from a ventilator, speech-language pathologists must appreciate the interaction between respiration and swallowing. Impairment in these systems is closely linked, due to the potential influences of upper airway flow and pressure on normal swallowing physiology. In conjunction with other co-morbidities of chronic illness, such as recurrent infections and decreased nutrition, the loss of consistent upper airway flow affects the ventilator weaning process. As a team member, the speech-language pathologist supports the communication and swallowing needs of patients, facilitating these processes throughout recovery and during movement toward liberation from mechanical ventilation.
Drugs and Dysphagia
Authors: Carl Lynette , Johnson Peter
Published: December 2008

This article summarizes some of the major medications that may affect eating and swallowing. The medications affecting motor function, lubrication, and gastrointestinal motility are discussed. The roles of medications in taste and smell are also identified in this paper.
Effect of the geometric phase on nuclear dynamics at a conical intersection: Extension of a recent topological approach from one to two coupled surfaces
Authors: Althorpe Stuart C. , Stecher Thomas , Bouakline Foudhil
Published: December 2008

A recent approach [S. C. Althorpe, J. Chem. Phys. 124, 084105 (2006)] for interpreting geometric phase (GP) effects in a nuclear wave function confined to the lower of two conically intersecting potential energy surfaces is extended to treat coupled dynamics on both surfaces. The approach is exact, and uses simple topology to separate the wave function into contributions from Feynman paths that wind different numbers of times, and in different senses, around the conical intersection. We derive the approach first, by mapping the time-dependent wave packet describing the coupled dynamics onto a double space, and second, by classifying the Feynman paths within a time-ordered expansion of the path integral. The approach is demonstrated numerically for a simple E×e Jahn–Teller system and for a model of the B11−S0 intersection in pyrrole. The approach allows one to investigate and interpret the effect of the GP on population transfer between the surfaces, and also to extract contributions to the coupled nuclear wave function from different reaction paths.
A Bayesian statistics approach to multiscale coarse graining
Authors: Liu Pu , Shi Qiang , Daumé Hal , Voth Gregory A.
Published: December 2008

Coarse-grained (CG) modeling provides a promising way to investigate many important physical and biological phenomena over large spatial and temporal scales. The multiscale coarse-graining (MS-CG) method has been proven to be a thermodynamically consistent way to systematically derive a CG model from atomistic force information, as shown in a variety of systems, ranging from simple liquids to proteins embedded in lipid bilayers. In the present work, Bayes’ theorem, an advanced statistical tool widely used in signal processing and pattern recognition, is adopted to further improve the MS-CG force field obtained from the CG modeling. This approach can regularize the linear equation resulting from the underlying force-matching methodology, therefore substantially improving the quality of the MS-CG force field, especially for the regions with limited sampling. Moreover, this Bayesian approach can naturally provide an error estimation for each force field parameter, from which one can know the extent the results can be trusted. The robustness and accuracy of the Bayesian MS-CG algorithm is demonstrated for three different systems, including simple liquid methanol, polyalanine peptide solvated in explicit water, and a much more complicated peptide assembly with 32 NNQQNY hexapeptides.
Anomalous training effect of perpendicular exchange bias in Pt/Co/Pt/IrMn multilayers
Authors: Shi Z. , Qiu X. P. , Zhou S. M. , Bai X. J. , Du J.
Published: December 2008

For perpendicularly magnetized Pt/Co/Pt and Pt/Co/Pt/IrMn multilayers, the magnetization reversal process is accompanied by the pinned domain wall motion. For Pt/Co/Pt/IrMn multilayers, the asymmetry of hysteresis loops is always equal to zero and the exchange field HE decreases during consecutive hysteresis loops. It is interesting to find that the variation in HE with the cycle number n cannot be fitted by the empirical 1/n function. Meanwhile, the coercivity almost does not change. The unique feature of the training effect is caused by the magnetization reversal mechanism of the pinned domain wall motion in the Pt/Co/Pt multilayers.
Bulk photoconductive gain in pentacene thin films
Authors: Gao J. , Hegmann F. A.
Published: December 2008

Bulk photoconductive gain greater than 16 is observed in pentacene thin films deposited onto coplanar interdigitated-electrode photodetector structures. The gain is highest at low light intensity but decreases at higher light intensity due to trap filling effects. The internal photogeneration quantum efficiency is found to be independent of wavelength below the absorption edge with the onset of photocurrent yield occurring at the absorption edge of the film.
Stabilization of HIF-1α is critical to improve wound healing in diabetic mice
Authors: Botusan Ileana Ruxandra , Sunkari Vivekananda Gupta , Savu Octavian , Catrina Anca Irinel , Grünler Jacob , Lindberg Stina , Pereira Teresa , Ylä-Herttuala Seppo , Poellinger Lorenz , Brismar Kerstin , Catrina Sergiu-Bogdan
Published: December 2008

Relative hypoxia is essential in wound healing since it normally plays a pivotal role in regulation of all the critical processes involved in tissue repair. Hypoxia-inducible factor (HIF) 1α is the critical transcription factor that regulates adaptive responses to hypoxia. HIF-1α stability and function is regulated by oxygen-dependent soluble hydroxylases targeting critical proline and asparaginyl residues. Here we show that hyperglycemia complexly affects both HIF-1α stability and activation, resulting in suppression of expression of HIF-1 target genes essential for wound healing both
in vitro
and
in vivo
. However, by blocking HIF-1α hydroxylation through chemical inhibition, it is possible to reverse this negative effect of hyperglycemia and to improve the wound healing process (i.e., granulation, vascularization, epidermal regeneration, and recruitment of endothelial precursors). Local adenovirus-mediated transfer of two stable HIF constructs demonstrated that stabilization of HIF-1α is necessary and sufficient for promoting wound healing in a diabetic environment. Our findings outline the necessity to develop specific hydroxylase inhibitors as therapeutic agents for chronic diabetes wounds. In conclusion, we demonstrate that impaired regulation of HIF-1α is essential for the development of diabetic wounds, and we provide evidence that stabilization of HIF-1α is critical to reverse the pathological process.
Prolyl hydroxylase inhibition during hyperoxia prevents oxygen-induced retinopathy
Authors: Sears Jonathan E. , Hoppe George , Ebrahem Quteba , Anand-Apte Bela
Published: December 2008

Oxygen-induced retinopathy (OIR) in the mouse, like the analogous human disease retinopathy of prematurity, is an ischemic retinopathy dependent on oxygen-induced vascular obliteration. We tested the hypothesis that chemically overriding the oxygen-induced downregulation of hypoxia-inducible factor (HIF) activity would prevent vascular obliteration and subsequent pathologic neovascularization in the OIR model. Because the degradation of HIF-1α is regulated by prolyl hydroxylases, we examined the effect of systemic administration of a prolyl hydroxylase inhibitor, dimethyloxalylglycine, in the OIR model. Our results determine that stabilizing HIF activity in the early phase of OIR prevents the oxygen-induced central vessel loss and subsequent vascular tortuosity and tufting that is characteristic of OIR. Overall, these findings imply that simulating hypoxia chemically by stabilizing HIF activity during the causative ischemia phase (hyperoxia) of retinopathy of prematurity may be of therapeutic value in preventing progression to the proliferative stage of the disease.
Endogenous methyl palmitate modulates nicotinic receptor-mediated transmission in the superior cervical ganglion
Authors: Wen Lin Hung , Liu Chao-Zong , Cao Deshou , Chen Po-Yi , Chen Mei-Fang , Lin Shinn-Zong , Mozayan Mansoor , Chen Alex F. , Premkumar Louis S. , Torry Donald S. , Lee Tony J.-F.
Published: December 2008

Nitric oxide (NO) is identified as the endothelium-derived relaxing factor and a neurotransmitter with a superfusion bioassay cascade technique. By using a similar technique with rat superior cervical ganglion (SCG) as donor tissue and rabbit endothelium-denuded aortic ring as detector tissue, we report here that a vasodilator, which is more potent than NO, is released in the SCG upon field electrical stimulation (FES) or addition of nicotine. Release of this vasodilator was enhanced by arginine analogs, includingNω-nitro-l-arginine (a NO synthase inhibitor), suggesting that it is not NO. Analysis by gas chromatography/mass spectrometry identified 2 saturated fatty acids, palmitic acid methyl ester (PAME) and stearic acid methyl ester (SAME), being released from the SCG upon FES in the presence of arginine analogs. Exogenous PAME but not SAME induced significant aortic dilation (EC50= 0.19 nM), indicating that PAME is the potent vasodilator. Release of PAME and SAME was significantly diminished in chronically decentralized SCG but not denervated SCG, suggesting the preganglionic origin. Furthermore, release of both fatty acids was calcium- and myosin light chain kinase-dependent, suggesting that both were released from axoplasmic vesicular stores. Electrophysiological studies further demonstrated that PAME but not SAME inhibited nicotine-induced inward currents in cultured SCG and the α7-nicotinic acetylcholine receptor-expressingXenopusoocytes. Endogenous PAME appears to play a role in modulation of the autonomic ganglionic transmission and to complement the vasodilator effect of NO.
Exemplars, Prototypes, Similarities, and Rules in Category Representation: An Example of Hierarchical Bayesian Analysis
Authors: Lee Michael D. , Vanpaemel Wolf
Published: December 2008

This article demonstrates the potential of using hierarchical Bayesian methods to relate models and data in the cognitive sciences. This is done using a worked example that considers an existing model of category representation, the Varying Abstraction Model (VAM), which attempts to infer the representations people use from their behavior in category learning tasks. The VAM allows for a wide variety of category representations to be inferred, but this article shows how a hierarchical Bayesian analysis can provide a unifying explanation of the representational possibilities using 2 parameters. One parameter controls the emphasis on abstraction in category representations, and the other controls the emphasis on similarity. Using 30 previously published data sets, this work shows how inferences about these parameters, and about the category representations they generate, can be used to evaluate data in terms of the ongoing exemplar versus prototype and similarity versus rules debates in the literature. Using this concrete example, this article emphasizes the advantages of hierarchical Bayesian models in converting model selection problems to parameter estimation problems, and providing one way of specifying theoretically based priors for competing models.
Comparison of Decision Learning Models Using the Generalization Criterion Method
Authors: Ahn Woo‐Young , Busemeyer Jerome R. , Wagenmakers Eric‐Jan , Stout Julie C.
Published: December 2008

It is a hallmark of a good model to make accurate a priori predictions to new conditions (). This study compared 8 decision learning models with respect to their generalizability. Participants performed 2 tasks (the Iowa Gambling Task and the Soochow Gambling Task), and each model made a priori predictions by estimating the parameters for each participant from 1 task and using those same parameters to predict on the other task. Three methods were used to evaluate the models at the individual level of analysis. The first method used a post hoc fit criterion, the second method used a generalization criterion for short‐term predictions, and the third method again used a generalization criterion for long‐term predictions. The results suggest that the models with the prospect utility function can make generalizable predictions to new conditions, and different learning models are needed for making short‐versus long‐term predictions on simple gambling tasks.
A Survey of Model Evaluation Approaches With a Tutorial on Hierarchical Bayesian Methods
Authors: Shiffrin Richard M. , Lee Michael D. , Kim Woojae , Wagenmakers Eric‐Jan
Published: December 2008

This article reviews current methods for evaluating models in the cognitive sciences, including theoretically based approaches, such as Bayes factors and minimum description length measures; simulation approaches, including model mimicry evaluations; and practical approaches, such as validation and generalization measures. This article argues that, although often useful in specific settings, most of these approaches are limited in their ability to give a general assessment of models. This article argues that hierarchical methods, generally, and hierarchical Bayesian methods, specifically, can provide a more thorough evaluation of models in the cognitive sciences. This article presents two worked examples of hierarchical Bayesian analyses to demonstrate how the approach addresses key questions of descriptive adequacy, parameter interference, prediction, and generalization in principled and coherent ways.
Ability, Breadth, and Parsimony in Computational Models of Higher‐Order Cognition
Authors: Cassimatis Nicholas L. , Bello Paul , Langley Pat
Published: December 2008

Computational models will play an important role in our understanding of human higher‐order cognition. How can a model's contribution to this goal be evaluated? This article argues that three important aspects of a model of higher‐order cognition to evaluate are (a) its ability to reason, solve problems, converse, and learn as well as people do; (b) the breadth of situations in which it can do so; and (c) the parsimony of the mechanisms it posits. This article argues that fits of models to quantitative experimental data, although valuable for other reasons, do not address these criteria. Further, using analogies with other sciences, the history of cognitive science, and examples from modern‐day research programs, this article identifies five activities that have been demonstrated to play an important role in our understanding of human higher‐order cognition. These include modeling within a cognitive architecture, conducting artificial intelligence research, measuring and expanding a model's ability, finding mappings between the structure of different domains, and attempting to explain multiple phenomena within a single model.
Disruption of the lower food web in Lake Ontario: Did it affect alewife growth or condition?
Authors: O'Gorman R. , Prindle S. E. , Lantry J. R. , Lantry B. F.
Published: December 2008

From the early 1980s to the late 1990s, a succession of non-native invertebrates colonized Lake Ontario and the suite of consequences caused by their colonization became known as “food web disruption”. For example, the native burrowing amphipod Diporeia spp., a key link in the profundal food web, declined to near absence, exotic predaceous cladocerans with long spines proliferated, altering the zooplankton community, and depth distributions of fishes shifted. These changes had the potential to affect growth and condition of planktivorous alewife Alosa pseudoharengus, the most abundant fish in the lake. To determine if food web disruption affected alewife, we used change-point analysis to examine alewife growth and adult alewife condition during 1976–2006 and analysis-of-variance to determine if values between change points differed significantly. There were no change points in growth during the first year of life. Of three change points in growth during the second year of life, one coincided with the shift in springtime distribution of alewife to deeper water but it was not associated with a significant change in growth. After the second year of life, no change points in growth were evident, although growth in the third year of life spiked in those years when Bythotrephes, the largest of the exotic cladocerans, was abundant suggesting that it was a profitable prey item for age-2 fish. We detected two change points in condition of adult alewife in fall, but the first occurred in 1981, well before disruption began. A second change point occurred in 2003, well after disruption began. After the springtime distribution of alewife shifted deeper during 1992–1994, growth in the first two years of life became more variable, and growth in years of life two and older became correlated (P < 0.05). In conclusion, food web disruption had no negative affect on growth and condition of alewife in Lake Ontario although it appears to have resulted in growth in the first two years of life becoming more variable, growth in years of life two and older becoming correlated (P < 0.05), and growth spurts in year of life three.
Observations on macrobenthic invertebrates and wader bird assemblages in a protected marine mudflat in Bahrain
Authors: Al-Sayed Hashim , Naser Humood , Al-Wedaei Khalil
Published: December 2008

Intertidal mudflats in Bahrain provide essential feeding grounds for a good number of shorebirds. The spatial distribution of soft-sediment macrobenthic invertebrate assemblages inhabiting a mudflat designated as a natural marine protected area was investigated to characterize shorebird food supplies. Molluscs accounted for 88% of the total macroinvertebrates community, reflecting a dominance of gastropod grazers. Six species of wading birds were recorded feeding in the protected area. Bird disturbance associated with human recreational activities that may interfere with the conservational benefits of this protected area was explored. This study highlighted the crucial need for management plans for protected areas and for further research concerning bird disturbance.
The distribution of the invasive New Zealand mud snail (Potamopyrgus antipodarum) in Lake Ontario
Authors: Levri Edward P. , Dermott Ron M. , Lunnen Shane J. , Kelly Ashley A. , Ladson Thomas
Published: December 2008

The invasive New Zealand mud snail, Potamopyrgus antipodarum, is a world-wide invasive species currently found in Europe, Australia, Japan, and, most recently, North America. It was first discovered in Lake Ontario in 1991. The purposes of this study were to update the current known geographic distribution of the snail, determine the relationship between depth and population densities, and examine the relationship between Potamopyrgus and dreissenid mussel densities in Lake Ontario. We sampled several locations in Lake Ontario and determined that the range of Potamopyrgus has expanded. However, densities appear to have moderated in the past ten years. In one location (Wilson, NY), the densities of the snail are dependent upon depth with highest densities occurring between 15 and 25 m. At this location, no snails were found at depths of less than 15 m. We found no correlation between the densities of Potamopyrgus and invasive mussels. The reasons for apparent reduction in densities over time and the apparent lack of Potamopyrgus in shallow water are discussed.
Phytoplankton community assessment in eight Lake Ontario tributaries made using fluorimetric methods
Authors: Twiss Michael R. , MacLeod Ian R.
Published: December 2008

Coastal inputs of nutrients and contaminants impact phytoplankton community composition and health in localized and large areas of coastal Lake Ontario. Advanced fluorimetric instrumentation (Fast Repetition Rate Fluorimeter [FRRF], FluoroProbe) was used during June 2006 to assess the in situ phytoplankton community of eight tributaries of Lake Ontario (Chaumont Bay, Sacketts Harbor/Black River, Oswego River, Port Bay, Sodus Bay, Irondequoit Bay, Genesee River, and Eighteen Mile Creek) representing a range of geomorphological features (rivers, protected embayments, open embayments). The instrumentation enabled high resolution (160 m) continuous monitoring of phytoplankton community composition (FluoroProbe) and photosynthetic efficiency (FRRF) along 1 m deep transect from nearshore (coastal Lake Ontario, > 7 m depth) to inshore (within the tributary, < 7 m depth). Limnological parameters such as water temperature, colored dissolved organic matter content (CDOM), total phosporus, nitrate, chloride, light extinction coefficient, and extracted size fractionated (0.2–2 μ m, 2–20 μ m, > 20 μ m) chlorophyll a concentrations were also determined. Results from this study illustrate the strong environmental gradients that exist along tributary transition zones into Lake Ontario. Offshore water quality was homogeneous and reflected nutrients levels (e.g. total phosphorus) that were below the Great Lakes Water Quality Agreement target value (10 μ g per litre), whereas most tributary inputs had elevated nutrient and chloride levels. Phytoplankton community composition differed between inshore and offshore sites and the transition coincided with changing water quality (followed using water temperature and CDOM concentrations) at the interface of the surface water masses. The greatest observed photosynthetic efficiencies occurred in the inshore environment; this is attributed to the greater nutrient availability rather than lower light levels. Fluorimetric applications provide useful techniques for monitoring water quality. Given the observed diversity of phytoplankton community and health among these tributary inputs, it follows that monitoring capabilities using the instrumentation applied here should be enhanced to observe these systems.
Fish larvae assemblage of a coastal area under influence of petrochemical activities, in Todos os Santos Bay, Bahia, Brazil
Authors: Mafalda P. , Souza C. S. , Velame M. P. B.
Published: December 2008

Todos os Santos Bay, having an area of approximately 927 km2, is the largest Bay on the Brazilian coast. Four sampling surveys, in two rainy and two dry periods, were made at five locations of Todos os Santos Bay, Bahia, Brazil, aiming to identify environmental and ecotoxicological correlates of ichthyoplankton assemblage structure. The study area showed a community characterised by the domination of Engraulididae, Gobiidae (Gobionellus spp.), Gerreidae (Diapterus spp. and Eucinostomus spp.) and Carangidae (Oligoplites spp. and Caranx spp.) larvae. There wasn't a significant difference in composition of fish larvae between the sampling periods, but there was a significant temporal variability in the most important environmental variables. The results showed statistically significant differences between northern stations and the control site, only for ammonium–nitrogen and total fish larvae density. The environmental variables (temperature, ammonium-nitrogen, oil and grease and chlorophyll a) explained 94.7% of the variation of the larval fish assemblage.
Derivation of free-boundary equilibrium linear models by a flux perturbation method
Authors: Bettini P. , Cavinato M. , Portone A.
Published: December 2008

A new method to derive linear models of the axisymmetric plasma dynamic is detailed. The method follows the modified inductance approach but adopts a different set of independent variables to perturb the equilibrium. This different basis permits one to reduce the numerical computation of the model and has revealed an interesting property of the inverse inductance matrix whose elements are influenced by the plasma only if they refer to circuits facing directly the plasma column. In terms of approximations, the method proposed is equivalent to the standard modified inductance method but has the additional advantage of ensuring numerical convergence of the perturbed equilibria and therefore it allows using Picard based numerical Grad–Shafranov solvers. A linear model of the RFX-mod machine was derived with this approach and it was validated against the experiment.
AY-WB Phytoplasma Secretes a Protein That Targets Plant Cell Nuclei
Authors: Bai Xiaodong , Correa Valdir R. , Toruño Tania Y. , Ammar El-Desouky , Kamoun Sophien , Hogenhout Saskia A.
Published: December 2008

The fully sequenced genome of aster yellows phytoplasma strain witches' broom (AY-WB; Candidatus Phytoplasma asteris) was mined for the presence of genes encoding secreted proteins based on the presence of N-terminal signal peptides (SP). We identified 56 secreted AY-WB proteins (SAP). These SAP are candidate effector proteins potentially involved in interaction with plant and insect cell components. One of these SAP, SAP11, contains an N-terminal SP sequence and a eukaryotic bipartite nuclear localization signal (NLS). Transcripts for SAP11 were detected in AY-WB-infected plants. Yellow fluorescence protein (YFP)-tagged SAP11 accumulated in Nicotiana benthamiana cell nuclei, whereas the nuclear targeting of YFP-tagged SAP11 mutants with disrupted NLS was inhibited. The nuclear transport of YFP-SAP11 was also inhibited in N. benthamiana plants in which the expression of importin α was knocked down using virus-induced gene silencing (VIGS). Furthermore, SAP11 was detected by immunocytology in nuclei of young sink tissues of China aster plants infected with AY-WB. In summary, this work shows that AY-WB phytoplasma produces a protein that targets the nuclei of plant host cells; this protein is a potential phytoplasma effector that may alter plant cell physiology.
A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000
Authors: Almeida Nalvo F. , Yan Shuangchun , Lindeberg Magdalen , Studholme David J. , Schneider David J. , Condon Bradford , Liu Haijie , Viana Carlos J. , Warren Andrew , Evans Clive , Kemen Eric , MacLean Dan , Angot Aurelie , Martin Gregory B. , Jones Jonathan D. , Collmer Alan , Setubal Joao C. , Vinatzer Boris A.
Published: December 2008

Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains and plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those interactions governing pathogen-host specificity. Comparative genomics of closely related pathogens with different host specificity represents an excellent approach for identification of genes contributing to host-range determination. A draft genome sequence of Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and compared with the genome of the closely related A. thaliana and tomato model pathogen P. syringae pv. tomato DC3000. Although the overall genetic content of each of the two genomes appears to be highly similar, the repertoire of effectors was found to diverge significantly. Several P. syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed to be translocated into plants, with the well-studied effector AvrRpt2 representing a likely candidate for host-range determination. However, the presence of avrRpt2 was not found sufficient to explain A. thaliana resistance to P. syringae pv. tomato T1, suggesting that other effectors and possibly type III secretion system–independent factors also play a role in this interaction.
Multiple Adhesin-Like Functions of Xanthomonas oryzae pv. oryzae Are Involved in Promoting Leaf Attachment, Entry, and Virulence on Rice
Authors: Das Amit , Rangaraj Nandini , Sonti Ramesh V.
Published: December 2008

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight of rice. We have used enhanced green fluorescent protein-tagged X. oryzae pv. oryzae cells in conjunction with confocal microscopy to monitor the role of several adhesin-like functions in bacterial adhesion to leaf surface and early stages of leaf entry. Mutations in genes encoding either the Xanthomonas adhesin-like protein A (XadA) or its paralog, Xanthomonas adhesin-like protein B (XadB), as well as the X. oryzae pv. oryzae homolog of Yersinia autotransporter-like protein H (YapH), exhibit deficiencies in leaf attachment or entry. A mutation in the X. oryzae pv. oryzae pilQ gene, which is predicted to encode the type IV pilus secretin, appears to have no effect on leaf attachment or entry. The xadA– mutant is deficient in the ability to cause disease following surface inoculation while the XadB, YapH, and PilQ functions are less important than XadA for this process. The xadA– and xadB– mutants have no effect on virulence following wound inoculation whereas the yapH– and pilQ– mutants are always virulence deficient following wound inoculation. Overall, these results indicate that multiple adhesin-like functions are involved in promoting virulence of X. oryzae pv. oryzae, with preferential involvement of individual functions at different stages of the disease process.
ERCC1 codon 118 C→T polymorphism associated with ERCC1 expression and outcome of FOLFOX‐4 treatment in Asian patients with metastatic colorectal carcinoma
Authors: Chang Peter Mu‐Hsin , Tzeng Cheng‐Hwai , Chen Po‐Min , Lin Jen‐Kou , Lin Tzu‐Chen , Chen Wei‐Shone , Jiang Jeng‐Kae , Wang Huann‐Sheng , Wang Wei‐Shu
Published: December 2008

We analyzed the influence of codon 118 C→T polymorphism of ERCC1 on its protein expression levels, clinicopathological features, and outcome of 168 Chinese patients with metastatic colorectal carcinoma that had been treated with first‐line FOLFOX‐4 chemotherapy. A high prevalence of C/C genotype was noted (47.6%, n = 80; 168 patients in total). A marked increase of ERCC1 protein expression levels was also noted in patients with C/T or T/T genotypes (70%vs 20%; P < 0.01), which was associated with significantly lower response to FOLFOX‐4 (36.4%vs 57.5%; p = 0.01), and shorter progression‐free (7 months vs 13 months; P < 0.01) and overall (16 months vs 25 months; P < 0.01) survival times. By multivariate analysis, this polymorphism was also identified as an independent prognostic factor (P = 0.02). These data suggest that Asian populations have a significantly higher prevalence of the C/C genotype in ERCC1 codon 118, which could be a key determinant for good responses to oxaliplatin‐based treatment and favorable outcomes. (Cancer Sci 2009; 100: 278–283)
Impact of alcohol consumption with polymorphisms in alcohol‐metabolizing enzymes on pancreatic cancer risk in Japanese
Authors: Kanda Junya , Matsuo Keitaro , Suzuki Takeshi , Kawase Takakazu , Hiraki Akio , Watanabe Miki , Mizuno Nobumasa , Sawaki Akira , Yamao Kenji , Tajima Kazuo , Tanaka Hideo
Published: December 2008

The putative impact of alcohol on pancreatic cancer (PC) risk remains controversial. Here, we conducted a case‐control study in Japanese to assess the impact of alcohol in conjunction with polymorphisms in alcohol‐metabolizing enzymes. Cases were 160 patients with pancreatic cancer at Aichi Cancer Center, Nagoya, Japan. Two control groups of 800 age‐ and sex‐matched non‐cancer subjects each were independently selected. The impact of alcohol and polymorphisms in aldehyde dehydrogenase 2 (ALDH2) Glu504Lys, alcohol dehydrogenase (ADH) 1B His48Arg, and ADH1C Arg272Gln on PC risk was examined with multivariate analysis adjusted for potential confounders to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Results showed no independent impact of alcohol or genotype on PC risk except former drinking. To avoid reverse causation, former drinkers were excluded in further analyses. In the analysis of the combined effects of alcohol consumption and genotype, significant impact of alcohol was seen for those subjects with ALDH2 Lys+ allele, ADH1B His/His, or ADH1C Arg/Arg (trend P = 0.077, 0.003, or 0.020, respectively), each of which is associated with a high concentration or rapid production of acetaldehyde. Analysis of genotype combinations showed that ‘ever drinking’ with both ADH1B His/His and ALDH2 Lys + was the most potent risk factor for PC relative to ‘never drinkers’ with both ADH1B His/His and ALDH2 Glu/Glu [OR (95% CI); 4.09 (1.30–12.85)]. These results indicate that alcohol has an impact on PC risk when the effects of alcohol consumption and metabolism are combined. Acetaldehyde may be involved in the mechanisms underlying PC development. (Cancer Sci 2009; 100: 296–302)
Warming of patients during Caesarean section: a telephone survey*
Authors: Woolnough M. J. , Hemingway C. , Allam J. , Cox M. , Yentis S. M.
Published: December 2008

We contacted the duty obstetric anaesthetist in 219 of the 220 consultant‐led maternity units in the UK (99.5%) and asked about departmental and individual practice regarding temperature management during Caesarean section. Warming during elective Caesarean section was routine in 35 units (16%). Intravenous fluid warmers were available in 213 units (97%), forced air warmers were available in 211 (96%) and warming mattresses were available in 42 (19%). Only 18 (8%) departments had specific guidelines for temperature management during Caesarean section. Personal intra‐operative practice was variable, although all of those contacted would initiate some form of active temperature management after a mean (SD) volume of blood loss of 1282 (404) ml, length of surgery of 78 (24) min, or core body temperature (if measured) of median (IQR [range]), 36 (35.5–36 [34–37.2]) °C.
Effects of sevoflurane on QT parameters in children with congenital sensorineural hearing loss
Authors: Kim H. S. , Kim J. T. , Kim C. S. , Kim S. D. , Kim K. , Yum M. K.
Published: December 2008

Sevoflurane prolongs the QT interval (QTI). Patients with congenital sensorineural hearing loss (SNHL) often have a prolonged QTI. This study was to investigate the effects of sevoflurane on the QTI in SNHL and control children. Thirty patients with SNHL and 30 controls were studied. The corrected QT interval (QTc), interval from peak to end of T wave (Tp‐e) and QT variability index (QTVI) were analysed. QTc and Tp‐e were estimated by the average QTc and Tp‐e measured beat‐by‐beat for 15 min. Heart rate power spectral analysis was performed. In both groups, QTc and QTVI increased during anaesthesia, but Tp‐e did not change. There were no differences in QTc, QTVI, Tp‐e, low‐ and high‐frequency power between the two groups. In both groups, sevoflurane lengthened the QTc and QTVI intervals but not Tp‐e.
Variation in rapid sequence induction techniques: current practice in Wales
Authors: Koerber J. P. , Roberts G. E. W. , Whitaker R. , Thorpe C. M.
Published: December 2008

A questionnaire survey examining rapid sequence induction techniques was sent to all anaesthetists in Wales. The questionnaire presented five common clinical scenarios: emergency appendicectomy; elective knee arthroscopy with a symptomatic hiatus hernia; elective knee arthroscopy with an asymptomatic hiatus hernia; elective Caesarean section; and emergency laparotomy for bowel obstruction. Completed surveys were received from 421 anaesthetists, a 68% response rate. Rapid sequence induction was chosen by 398/400 respondents (100%) for bowel obstruction, 392/399 (98%) for Caesarean section, 388/408 (95%) for appendicectomy, 328/395 (83%) for symptomatic hiatus hernia but only 98/399 (25%) for asymptomatic hiatus hernia (p < 0.001). Trainees were more likely to use a rapid sequence induction technique than consultants and staff grades for the appendicectomy (p = 0.025), symptomatic hiatus hernia (p = 0.004) and asymptomatic hiatus hernia (p = 0.001) scenarios and were also more likely to use a thiopental–suxamethonium combination for rapid sequence induction (p < 0.001).
Evaluation of a new method of assessing depth of sedation using two‐choice visual reaction time testing on a mobile phone*
Authors: Thomson A. J. , Nimmo A. F. , Tiplady B. , Glen J. B.
Published: December 2008

The utility of two‐choice visual reaction time testing using a specially programmed mobile telephone as a measure of sedation level was investigated in 20 healthy patients sedated with target controlled infusions of propofol. At gradually increasing target concentrations visual reaction time was compared with patient‐assessed visual analogue scale sedation scores and an observer‐rated scale. Propofol sedation caused dose‐dependent increases in visual reaction time and visual analogue scale scores that were statistically significant when the calculated effect‐site concentration reached 0.9 μg.ml−1 (p < 0.05) and 0.5 μg.ml−1 (p < 0.01) respectively. While visual analogue scale scores were more sensitive at lower levels of sedation than visual reaction time, the latter demonstrated marked increase in values at higher levels of sedation. Visual reaction time may be useful for identifying impending over‐sedation.
Interscalene brachial plexus block: assessment of the needle angle needed to enter the spinal canal*
Authors: Russon K. E. , Herrick M. J. , Moriggl B. , Messner H. J. , Dixon A. , Harrop‐Griffiths W. , Denny N. M.
Published: December 2008

Attempts were made to place 8‐cm 22G needles into the spinal canals of four preserved cadavers using the skin entry point most commonly associated with the lateral interscalene brachial plexus block or Winnie approach (that is, at the level of the cricoid cartilage). Eleven successful attempts were confirmed by computed tomography. Needle angles that were cephalad, transverse or slightly caudad were associated with entry into the spinal canal at depths of 5.0 cm or less from the skin. The only needle entry into the spinal canal with a needle angle of > 50 degrees to the transverse plane (< 40 degrees to the sagittal plane) entered the intervertebral foramen at a depth of 7.7 cm from the skin. We conclude that the use of markedly caudad angulations of needles no longer than 5.0 cm may minimise the chances of spinal canal entry and spinal cord damage.
A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle
Authors: Hayes B. J. , Chamberlain A. J. , Maceachern S. , Savin K. , McPartlan H. , MacLeod I. , Sethuraman L. , Goddard M. E.
Published: December 2008

A number of cattle breeds have become highly specialized for milk or beef production, following strong artificial selection for these traits. In this paper, we compare allele frequencies from 9323 single nucleotide polymorphism (SNP) markers genotyped in dairy and beef cattle breeds averaged in sliding windows across the genome, with the aim of identifying divergently selected regions of the genome between the production types. The value of the method for identifying selection signatures was validated by four sources of evidence. First, differences in allele frequencies between dairy and beef cattle at individual SNPs were correlated with the effects of those SNPs on production traits. Secondly, large differences in allele frequencies generally occurred in the same location for two independent data sets (correlation 0.45) between sliding window averages. Thirdly, the largest differences in sliding window average difference in allele frequencies were found on chromosome 20 in the region of the growth hormone receptor gene, which carries a mutation known to have an effect on milk production traits in a number of dairy populations. Finally, for the chromosome tested, the location of selection signatures between dairy and beef cattle was correlated with the location of selection signatures within dairy cattle.