Application of altimetry data assimilation on mesoscale eddies simulation

Mesoscale eddy plays an important role in the ocean circulation. In order to improve the simulation accuracy of the mesoscale eddies, a three-dimensional variation (3DVAR) data assimilation system called Ocean Variational Analysis System (OVALS) is coupled with a POM model to simulate the mesoscale eddies in the Northwest Pacific Ocean. In this system, the sea surface height anomaly (SSHA) data by satellite altimeters are assimilated and translated into pseudo temperature and salinity (T-S) profile data. Then, these profile data are taken as observation data to be assimilated again and produce the three-dimensional analysis T-S field. According to the characteristics of mesoscale eddy, the most appropriate assimilation parameters are set up and testified in this system. A ten years mesoscale eddies simulation and comparison experiment is made, which includes two schemes: assimilation and non-assimilation. The results of comparison between two schemes and the observation show that the simulation accuracy of the assimilation scheme is much better than that of non-assimilation, which verified that the altimetry data assimilation method can improve the simulation accuracy of the mesoscale dramatically and indicates that it is possible to use this system on the forecast of mesoscale eddies in the future.

Restructuring Sparse High Dimensional Data for Effective Retrieval

The task in text retrieval is to find the subset of a collection of documents relevant to a user's information request, usually expressed as a set of words. Classically, documents and queries are represented as vectors of word counts. In its simplest form, relevance is defined to be the dot product between a document and a query vector--a measure of the number of common terms. A central difficulty in text retrieval is that the presence or absence of a word is not sufficient to determine relevance to a query. Linear dimensionality reduction has been proposed as a technique for extracting underlying structure from the document collection. In some domains (such as vision) dimensionality reduction reduces computational complexity. In text retrieval it is more often used to improve retrieval performance. We propose an alternative and novel technique that produces sparse representations constructed from sets of highly-related words. Documents and queries are represented by their distance to these sets. and relevance is measured by the number of common clusters. This technique significantly improves retrieval performance, is efficient to compute and shares properties with the optimal linear projection operator and the independent components of documents.

How does TCP generate Pseudo-self-similarity?

Long-range dependence has been observed in many recent Internet traffic measurements. In addition, some recent studies have shown that under certain network conditions, TCP itself can produce traffic that exhibits dependence over limited timescales, even in the absence of higher-level variability. In this paper, we use a simple Markovian model to argue that when the loss rate is relatively high, TCP's adaptive congestion control mechanism indeed generates traffic with OFF periods exhibiting power-law shape over several timescales and thus introduces pseudo-long-range dependence into the overall traffic. Moreover, we observe that more variable initial retransmission timeout values for different packets introduces more variable packet inter-arrival times, which increases the burstiness of the overall traffic. We can thus explain why a single TCP connection can produce a time-series that can be misidentified as self-similar using standard tests.

Synthesis and reactivity of α-diazo-β-keto sulfoxides: scope and synthetic potential

The research described in this thesis focuses on the design and synthesis of stable α-diazosulfoxides and investigation of their reactivity under a variety of conditions (transition-metal catalysis, thermal, photochemical and microwave) with a particular emphasis on the synthesis of novel heterocyclic compounds with potential biological activity. The exclusive reaction pathway for these α-diazosulfoxides was found to be hetero-Wolff rearrangement to give α-oxosulfine intermediates. In the first chapter, a literature review of sulfines is presented, including a discussion of naturally occurring sulfines, and an overview of the synthesis and reactivity of sulfines. The potential of sulfines in organic synthesis and recent developments in particular are highlighted. The second chapter discusses the synthesis and reactivity of α-diazosulfoxides, building on earlier results in this research group. The synthesis of lactone-based α-diazosulfoxides and, for the first time, ketone-based benzofused and monocyclic α-diazosulfoxides is described. The reactivity of these α-diazosulfoxides is then explored under a variety of conditions, such as transition-metal catalysis, photochemical and microwave, generating labile α-oxosulfine intermediates, which are trapped using amines and dienes, in addition to the spontaneous reaction pathways which occur with α-oxosulfines in the absence of a trap. A new reaction pathway was explored with the lactone based α-oxosulfines, involving reaction with amines to generate novel 3-aminofuran-2(5H)-ones via carbophilic attack, in very good yields. The reactivity of ketone-based α-diazosulfoxides was explored for the first time, and once again, pseudo-Wolff rearrangement to the α-oxosulfines was the exclusive reaction pathway observed. The intermediacy of the α-oxosulfines was confirmed by trapping as cycloadducts, with the stereochemical features dependant on the reaction conditions. In the absence of a diene trap, a number of reaction fates from the α-oxosulfines were observed, including complete sulfinyl extrusion to give indanones, sulfur extrusion to give indanediones, and, to a lesser extent, dimerisation. The indanediones were characterised by trapping as quinoxalines, to enable full characterisation. One of the overriding outcomes of this thesis was the provision of new insights into the behaviour of α-oxosulfines with different transition metal catalysts, and under thermal, microwave and photolysis conditions. A series of 3-aminofuran-2(5H)-ones and benzofused dihydro-2H-thiopyran S-oxides were submitted for anticancer screening at the U.S. National Cancer Institute. A number of these derivatives were identified as hit compounds, with excellent cell growth inhibition. One 3-aminofuran-2(5H)-one derivative has been chosen for further screening. The third chapter details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research. The data for the crystal structures are contained in the attached CD.

Quantifying data quality for clinical trials using electronic data capture.

BACKGROUND: Historically, only partial assessments of data quality have been performed in clinical trials, for which the most common method of measuring database error rates has been to compare the case report form (CRF) to database entries and count discrepancies. Importantly, errors arising from medical record abstraction and transcription are rarely evaluated as part of such quality assessments. Electronic Data Capture (EDC) technology has had a further impact, as paper CRFs typically leveraged for quality measurement are not used in EDC processes. METHODS AND PRINCIPAL FINDINGS: The National Institute on Drug Abuse Treatment Clinical Trials Network has developed, implemented, and evaluated methodology for holistically assessing data quality on EDC trials. We characterize the average source-to-database error rate (14.3 errors per 10,000 fields) for the first year of use of the new evaluation method. This error rate was significantly lower than the average of published error rates for source-to-database audits, and was similar to CRF-to-database error rates reported in the published literature. We attribute this largely to an absence of medical record abstraction on the trials we examined, and to an outpatient setting characterized by less acute patient conditions. CONCLUSIONS: Historically, medical record abstraction is the most significant source of error by an order of magnitude, and should be measured and managed during the course of clinical trials. Source-to-database error rates are highly dependent on the amount of structured data collection in the clinical setting and on the complexity of the medical record, dependencies that should be considered when developing data quality benchmarks.

Using the Continuous Plankton Recorder to investigate the absence of North Atlantic right whales (Eubalaena glacialis) from the Roseway Basin foraging ground

North Atlantic right whales (Eubalaena glacialis) were absent from Roseway Basin, located off southeastern Nova Scotia, for a 7-year period (1993–1999). The objective of this study was to examine the availability of the right whale's main prey, Calanus finmarchicus, in Roseway Basin during those 7 years to determine if the whales’ absence was due to inadequate prey resources. Since we had no historical data on zooplankton abundances at depth on the Scotian Shelf, near-surface zooplankton abundance data from the Continuous Plankton Recorder were used to infer water-column abundances. In addition, environmental parameters that are often correlated with high zooplankton concentrations were examined. The hypotheses tested were that changes in these parameters would be detectable between three time periods: pre-1993, 1993–1999 and post-1999. Calanus finmarchicus abundance was found to be lowest during 1993–1999, suggesting that right whales were not foraging in Roseway Basin because of the near-absence of their main prey species. Decreased in situ salinity and density proved to be indicators of the changes in circulation in the 1990s that may have affected the advection of C. finmarchicus onto the Scotian Shelf.

Absence of the 7-repeat variant of the DRD4 VNTR is associated with drifting sustained attention in children with ADHD but not in controls

Many genetic studies have demonstrated an association between the 7-repeat (7r) allele of a 48-base pair variable number of tandem repeats (VNTR) in exon 3 of the DRD4 gene and the phenotype of attention deficit hyperactivity disorder (ADHD). Previous studies have shown inconsistent associations between the 7r allele and neurocognitive performance in children with ADHD. We investigated the performance of 128 children with and without ADHD on the Fixed and Random versions of the Sustained Attention to Response Task (SART). We employed timeseries analyses of reaction-time data to allow a fine-grained analysis of reaction time variability, a candidate endophenotype for ADHD. Children were grouped into either the 7r-present group (possessing at least one copy of the 7r allele) or the 7r-absent group. The ADHD group made significantly more commission errors and was significantly more variable in RT in terms of fast moment-to-moment variability than the control group, but no effect of genotype was found on these measures. Children with ADHD without the 7r allele made significantly more omission errors, were significantly more variable in the slow frequency domain and showed less sensitivity to the signal (d') than those children with ADHD the 7r and control children with or without the 7r. These results highlight the utility of time-series analyses of reaction time data for delineating the neuropsychological deficits associated with ADHD and the DRD4 VNTR. Absence of the 7-repeat allele in children with ADHD is associated with a neurocognitive profile of drifting sustained attention that gives rise to variable and inconsistent performance. (c) 2008 Wiley-Liss, Inc.

Inhibition of Advanced Glycation and Absence of Galectin-3 Prevent Blood-Retinal Barrier Dysfunction during Short-Term Diabetes

Breakdown of the inner blood-retinal barrier (iBRB) occurs early in diabetes and is central to the development of sight-threatening diabetic macular edema (DME) as retinopathy progresses. In the current study, we examined how advanced glycation end products (AGEs) forming early in diabetes could modulate vasopermeability factor expression in the diabetic retina and alter inter-endothelial cell tight junction (TJ) integrity leading to iBRB dysfunction. We also investigated the potential for an AGE inhibitor to prevent this acute pathology and examined a role of the AGE-binding protein galectin-3 (Gal-3) in AGE-mediated cell retinal pathophysiology. Diabetes was induced in C57/BL6 wild-type (WT) mice and in Gal-3(-/-) transgenic mice. Blood glucose was monitored and AGE levels were quantified by ELISA and immunohistochemistry. The diabetic groups were subdivided, and one group was treated with the AGE-inhibitor pyridoxamine (PM) while separate groups of WT and Gal-3(-/-) mice were maintained as nondiabetic controls. iBRB integrity was assessed by Evans blue assay alongside visualisation of TJ protein complexes via occludin-1 immunolocalization in retinal flat mounts. Retinal expression levels of the vasopermeability factor VEGF were quantified using real-time RT-PCR and ELISA. WT diabetic mice showed significant AGE -immunoreactivity in the retinal microvasculature and also showed significant iBRB breakdown (P < .005). These diabetics had higher VEGF mRNA and protein expression in comparison to controls (P < .01). PM-treated diabetics had normal iBRB function and significantly reduced diabetes-mediated VEGF expression. Diabetic retinal vessels showed disrupted TJ integrity when compared to controls, while PM-treated diabetics demonstrated near-normal configuration. Gal-3(-/-) mice showed significantly less diabetes-mediated iBRB dysfunction, junctional disruption, and VEGF expression changes than their WT counterparts. The data suggests an AGE-mediated disruption of iBRB via upregulation of VEGF in the diabetic retina, possibly modulating disruption of TJ integrity, even after acute diabetes. Prevention of AGE formation or genetic deletion of Gal-3 can effectively prevent these acute diabetic retinopathy changes.

Investigating paediatric airways by non-bronchoscopic lavage: Normal cellular data

Background: Bronchoscopic bronchoalveolar lavage in children to investigate bronchia disorders such as asthtna has both ethical and procedural difficulties.


Objective: The aim of this study was to establish a standardized non-bronchoscopic method to perform bronchoalveolar lavage in children attending for elective surgery to obtain normal cellular data.


Methods: Bronchoalveolar lavage was performed on normal children (n= 55) by infusing saline (20 mL) through an 8 FG suction catheter passed after endotracheal intubation. Oxygen saturation, heart and respiratory rate were monitored during the bronchoalveolar lavage procedure. Cellular analysis and total protein estimation of the lavage fluid were performed. Epithelial lining fluid volume was calculated (n = 15) using the urea dilution method.


Results: The procedure was well tolerated by all children. Total cell count and differential cell count for children (macrophages 70.8 ± 2.3%, lymphocytes 3.8 ± 0.6%, neutrophils 5,7 ± 1.0%, eosinophils 0.14 ± 0.03%. epithelial cells 19.6 ± 2.1%, mast cells 0.21 ± 0.02%) were similar to those reported for adults. Age and sex comparisons revealed no differences between groups. The mean total protein recovered in the cell free supernatant was 49.72 ± 4.29 mg/L and epithelial lining fluid volume was 0.82 ± 0.11% of return lavageate.


Conclusion This method allows bronchoalveolar lavage to be performed safely and quickly on children attending for routine elective surgery. Using this method and taking the ‘window of opportunity’ of elective surgery, the presence or absence of airway inflammation could be studied in children with various patterns of asthma during relatively asymptomatic periods.

The Role of Work Group in Individual Sickness Absence Behavior

The purpose of our two-year follow-up study was to examine the effect of the social components of the work group, such as group absence norms and cohesion, on sickness absence behavior among individuals with varying attitudes toward work attendance. The social components were measured using a questionnaire survey, and data on sickness absence behavior were collected from the employers' records. The study population consisted of 19,306 Finnish municipal employees working in 1,847 groups (78% women). Multilevel Poisson regression modeling was applied. The direct effects of work group characteristics on sickness absence were mostly insignificant. In contrast, both of the social components of a work group had an indirect impact: The more tolerant the group absence norms (at both individual- and cross-level) and the lower the group cohesion (at the individual level), the more the absence behavior of an individual was influenced by his or her attitude toward work attendance. We conclude that work group moderates the extent to which individuals with a liberal attitude toward work attendance actually engage in sickness absence behavior.

Regression analysis of spatial data

Many of the most interesting questions ecologists ask lead to analyses of spatial data. Yet, perhaps confused by the large number of statistical models and fitting methods available, many ecologists seem to believe this is best left to specialists. Here, we describe the issues that need consideration when analysing spatial data and illustrate these using simulation studies. Our comparative analysis involves using methods including generalized least squares, spatial filters, wavelet revised models, conditional autoregressive models and generalized additive mixed models to estimate regression coefficients from synthetic but realistic data sets, including some which violate standard regression assumptions. We assess the performance of each method using two measures and using statistical error rates for model selection. Methods that performed well included generalized least squares family of models and a Bayesian implementation of the conditional auto-regressive model. Ordinary least squares also performed adequately in the absence of model selection, but had poorly controlled Type I error rates and so did not show the improvements in performance under model selection when using the above methods. Removing large-scale spatial trends in the response led to poor performance. These are empirical results; hence extrapolation of these findings to other situations should be performed cautiously. Nevertheless, our simulation-based approach provides much stronger evidence for comparative analysis than assessments based on single or small numbers of data sets, and should be considered a necessary foundation for statements of this type in future.

Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data

Diagnostic test sensitivity and specificity are probabilistic estimates with far reaching implications for disease control, management and genetic studies. In the absence of 'gold standard' tests, traditional Bayesian latent class models may be used to assess diagnostic test accuracies through the comparison of two or more tests performed on the same groups of individuals. The aim of this study was to extend such models to estimate diagnostic test parameters and true cohort-specific prevalence, using disease surveillance data. The traditional Hui-Walter latent class methodology was extended to allow for features seen in such data, including (i) unrecorded data (i.e. data for a second test available only on a subset of the sampled population) and (ii) cohort-specific sensitivities and specificities. The model was applied with and without the modelling of conditional dependence between tests. The utility of the extended model was demonstrated through application to bovine tuberculosis surveillance data from Northern and the Republic of Ireland. Simulation coupled with re-sampling techniques, demonstrated that the extended model has good predictive power to estimate the diagnostic parameters and true herd-level prevalence from surveillance data. Our methodology can aid in the interpretation of disease surveillance data, and the results can potentially refine disease control strategies.

Compositional data-driven alternatives to single geochemical component maps

Conventional practice in Regional Geochemistry includes as a final step of any geochemical campaign the generation of a series of maps, to show the spatial distribution of each of the components considered. Such maps, though necessary, do not comply with the compositional, relative nature of the data, which unfortunately make any conclusion based on them sensitive
to spurious correlation problems. This is one of the reasons why these maps are never interpreted isolated. This contribution aims at gathering a series of statistical methods to produce individual maps of multiplicative combinations of components (logcontrasts), much in the flavor of equilibrium constants, which are designed on purpose to capture certain aspects of the data.
We distinguish between supervised and unsupervised methods, where the first require an external, non-compositional variable (besides the compositional geochemical information) available in an analogous training set. This external variable can be a quantity (soil density, collocated magnetics, collocated ratio of Th/U spectral gamma counts, proportion of clay particle fraction, etc) or a category (rock type, land use type, etc). In the supervised methods, a regression-like model between the external variable and the geochemical composition is derived in the training set, and then this model is mapped on the whole region. This case is illustrated with the Tellus dataset, covering Northern Ireland at a density of 1 soil sample per 2 square km, where we map the presence of blanket peat and the underlying geology. The unsupervised methods considered include principal components and principal balances
(Pawlowsky-Glahn et al., CoDaWork2013), i.e. logcontrasts of the data that are devised to capture very large variability or else be quasi-constant. Using the Tellus dataset again, it is found that geological features are highlighted by the quasi-constant ratios Hf/Nb and their ratio against SiO2; Rb/K2O and Zr/Na2O and the balance between these two groups of two variables; the balance of Al2O3 and TiO2 vs. MgO; or the balance of Cr, Ni and Co vs. V and Fe2O3. The largest variability appears to be related to the presence/absence of peat.

An R -matrix with pseudo-states calculation of electron-impact excitation in C 2 +

We have performed an R-matrix with pseudo-states (RMPS) calculation of electron-impact excitation in C2+.Collision strengths and effective collision strengths were determined for excitation between the lowest 24 terms, including all those arising from the 2s3l and 2s4l configurations. In the RMPS calculation, 238 terms (90 spectroscopic and 148 pseudo-state) were employed in the close-coupling (CC) expansion of the target. In order to investigate the significance of coupling to the target continuum and highly excited bound states, we compare the RMPS results with those from an R-matrix calculation that incorporated all 238 terms in the configuration- interaction expansion, but only the lowest 44 spectroscopic terms in the CC expansion. We also compare our effective collision strengths with those from an earlier 12-state R-matrix calculation (Berrington et al 1989 J. Phys. B: At.Mol. Opt. Phys. 22 665). The RMPS calculation was extremely large, involving (N +1)-electron Hamiltonian matrices of dimension up to 36 085, and required the use of our recently completed suite of parallel R-matrix programs. The full set of effective collision strengths fromourRMPS calculation is available at theOakRidgeNationalLaboratoryControlledFusion Atomic Data Center web site. 1.

Generalized collisional radiative model for light elements. Part B: Data for the Be isonuclear sequence

A first-stage collision database is assembled which contains electron-impact excitation, ionization, and recombination rate coefficients for Be, Be+, Be2+, and Be3+. The first-stage database is constructed using the R-matrix with pseudo-states, time-dependent close-coupling, and perturbative, distorted-wave methods. A second-stage collision database is then assembled which contains generalized collisional-radiative and radiated power loss coefficients. The second-stage database is constructed by solution of collisional-radiative equations in the quasi-static equilibrium approximation using the first-stage database. Both collision database stages reside in electronic form at the ORNL Controlled Fusion Atomic Data Center and in the ADAS database, and are easily accessed over the worldwide internet. © 2007 Elsevier Inc. All rights reserved.