Sequence Changes in Six Variants of Rice Tungro Bacilliform Virus and Their Phylogenetic Relationships

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Drag coefficient in a crystal suspension

A single air bubble rising in xanthan gum crystal suspension has been studied experimentally. The suspension was made by different concentrations of xanthan gum solutions with 0.23 mm polystyrene crystal particles. Drag co-efficient data and a new correlation of drag coefficient is presented for spherical and nonspherical bubbles in non-Newtonian crystal suspension. The correlation is developed in terms of the Reynolds number, Re and the bubble shape factor, � (the ratio between the surface equivalent sphere diameter to the volume equivalent sphere diameter). The experimental drag coefficient was found to be consistent with this new predicted correlation and published data over the ranges, 0.1phi<2.5.

Krylov subspace approximations for the exponential Euler method: Error estimates and the harmonic Ritz approximant

We study Krylov subspace methods for approximating the matrix-function vector product φ(tA)b where φ(z) = [exp(z) - 1]/z. This product arises in the numerical integration of large stiff systems of differential equations by the Exponential Euler Method, where A is the Jacobian matrix of the system. Recently, this method has found application in the simulation of transport phenomena in porous media within mathematical models of wood drying and groundwater flow. We develop an a posteriori upper bound on the Krylov subspace approximation error and provide a new interpretation of a previously published error estimate. This leads to an alternative Krylov approximation to φ(tA)b, the so-called Harmonic Ritz approximant, which we find does not exhibit oscillatory behaviour of the residual error.

Sparse temporal representations for facial expression recognition

In automatic facial expression recognition, an increasing number of techniques had been proposed for in the literature that exploits the temporal nature of facial expressions. As all facial expressions are known to evolve over time, it is crucially important for a classifier to be capable of modelling their dynamics. We establish that the method of sparse representation (SR) classifiers proves to be a suitable candidate for this purpose, and subsequently propose a framework for expression dynamics to be efficiently incorporated into its current formulation. We additionally show that for the SR method to be applied effectively, then a certain threshold on image dimensionality must be enforced (unlike in facial recognition problems). Thirdly, we determined that recognition rates may be significantly influenced by the size of the projection matrix \Phi. To demonstrate these, a battery of experiments had been conducted on the CK+ dataset for the recognition of the seven prototypic expressions - anger, contempt, disgust, fear, happiness, sadness and surprise - and comparisons have been made between the proposed temporal-SR against the static-SR framework and state-of-the-art support vector machine.

Loss of breast epithelial marker hCLCA2 promotes epithelial to mesenchymal transition and indicates higher risk of metastasis

Transition between epithelial and mesenchymal states is a feature of both normal development and tumor progression. We report that expression of chloride channel accessory protein hCLCA2 is a characteristic of epithelial differentiation in the immortalized MCF10A and HMLE models, while induction of epithelial-to-mesenchymal transition by cell dilution, TGFβ or mesenchymal transcription factors sharply reduces hCLCA2 levels. Attenuation of hCLCA2 expression by lentiviral small hairpin RNA caused cell overgrowth and focus formation, enhanced migration and invasion, and increased mammosphere formation in methylcellulose. These changes were accompanied by downregulation of E-cadherin and upregulation of mesenchymal markers such as vimentin and fibronectin. Moreover, hCLCA2 expression is greatly downregulated in breast cancer cells with a mesenchymal or claudin-low profile. These observations suggest that loss of hCLCA2 may promote metastasis. We find that higher-than-median expression of hCLCA2 is associated with a one-third lower rate of metastasis over an 18-year period among breast cancer patients compared with lower-than-median (n=344, unfiltered for subtype). Thus, hCLCA2 is required for epithelial differentiation, and its loss during tumor progression contributes to metastasis. Overexpression of hCLCA2 has been reported to inhibit cell proliferation and is accompanied by increases in chloride current at the plasma membrane and reduced intracellular pH (pHi). We found that knockdown cells have sharply reduced chloride current and higher pHi, both characteristics of tumor cells. These results suggest a mechanism for the effects on differentiation. Loss of hCLCA2 may allow escape from pHi homeostatic mechanisms, permitting the higher intracellular and lower extracellular pH that are characteristic of aggressive tumor cells.

Isolation and characterization of charge-tagged phenylperoxyl radicals in the gas phase : direct evidence for products and pathways in low temperature benzene oxidation

The phenylperoxyl radical has long been accepted as a critical intermediate in the oxidation of benzene and an archetype for arylperoxyl radicals in combustion and atmospheric chemistry. Despite being central to many contemporary mechanisms underpinning these chemistries, reports of the direct detection or isolation of phenylperoxyl radicals are rare and there is little experimental evidence connecting this intermediate with expected product channels. We have prepared and isolated two charge-tagged phenyl radical models in the gas phase [i.e., 4-(N,N,N-trimethylammonium) phenyl radical cation and 4-carboxylatophenyl radical anion] and observed their reactions with dioxygen by ion-trap mass spectrometry. Measured reaction rates show good agreement with prior reports for the neutral system (k(2)[(Me3N+)C6H4 center dot + O-2] = 2.8 x 10(-11) cm(3) molecule(-1) s(-1), Phi = 4.9%; k(2)[(-O2C)C6H4 center dot + O-2] = 5.4 x 10(-1)1 cm(3) molecule(-1) s(-1), Phi = 9.2%) and the resulting mass spectra provide unequivocal evidence for the formation of phenylperoxyl radicals. Collisional activation of isolated phenylperoxyl radicals reveals unimolecular decomposition by three pathways: (i) loss of dioxygen to reform the initial phenyl radical; (ii) loss of atomic oxygen yielding a phenoxyl radical; and (iii) ejection of the formyl radical to give cyclopentadienone. Stable isotope labeling confirms these assignments. Quantum chemical calculations for both charge-tagged and neutral phenylperoxyl radicals confirm that loss of formyl radical is accessible both thermodynamically and entropically and competitive with direct loss of both hydrogen atom and carbon dioxide.

The impact of cataract surgery on vision-related quality of life for bilateral cataract patients in Ho Chi Minh City, Vietnam : a prospective study

Background To determine the impact of cataract surgery on vision-related quality of life (VRQOL) and examine the association between objective visual measures and change in VRQOL after surgery among bilateral cataract patients in Ho Chi Minh City, Vietnam. Methods A cohort of older patients with bilateral cataract was assessed one week before and one to three months after first eye or both eye cataract surgery. Visual measures including visual acuity, contrast sensitivity and stereopsis were obtained. Vision-related quality of life was assessed using the NEI VFQ-25. Descriptive analyses and a generalized linear estimating equation (GEE) analysis were undertaken to measure change in VRQOL after surgery. Results Four hundred and thirteen patients were assessed before cataract surgery and 247 completed the follow-up assessment one to three months after first or both eye cataract surgery. Overall, VRQOL significantly improved after cataract surgery (p < 0.001) particularly after both eye surgeries. Binocular contrast sensitivity (p < 0.001) and stereopsis (p < 0.001) were also associated with change in VRQOL after cataract surgery. Visual acuity was not associated with VRQOL. Conclusions Cataract surgery significantly improved VRQOL among bilateral cataract patients in Vietnam. Contrast sensitivity as well as stereopsis, rather than visual acuity significantly affected VRQOL after cataract surgery.

Prevalence and visual risk factors for falls in bilateral cataract patients in Ho Chi Minh City, Vietnam

Purpose To determine the prevalence of falls in the 12 months prior to cataract surgery and examine the associations between visual and other risk factors and falls among older bilateral cataract patients in Vietnam. Methods Data collected from 413 patients in the week before scheduled cataract surgery included a questionnaire and three objective visual tests. Results The outcome of interest was self-reported falls in the previous 12 months. A total of 13% (n = 53) of bilateral cataract patients reported 60 falls within the previous 12 months. After adjusting for age, sex, race, employment status, comorbidities, medication usage, refractive management, living status and the three objective visual tests in the worse eye, women (odds ratio, OR, 4.64, 95% confidence interval, CI, 1.85–11.66), and those who lived alone (OR 4.51, 95% CI 1.44–14.14) were at increased risk of a fall. Those who reported a comorbidity were at decreased risk of a fall (OR 0.43, 95% CI 0.19–0.95). Contrast sensitivity (OR 0.31, 95% CI 0.10–0.95) was the only significant visual test associated with a fall. These results were similar for the better eye, except the presence of a comorbidity was not significant (OR 0.45, 95% CI 0.20–1.02). Again, contrast sensitivity was the only significant visual factor associated with a fall (OR 0.15, 95% CI 0.04–0.53). Conclusion Bilateral cataract patients in Vietnam are potentially at high risk of falls and in need of falls prevention interventions. It may also be important for ophthalmologists and health professionals to consider contrast sensitivity measures when prioritizing cataract patients for surgery and assessing their risk of falls.

Measuring load of phosphate in the environment by passive sampling techniques: An introduction

Phosphorus has a number of indispensable biochemical roles, but its natural deposition and the low solubility of phosphates as well as their rapid transformation to insoluble forms make the element commonly the growth-limiting nutrient, particularly in aquatic ecosystems. Famously, phosphorus that reaches water bodies is commonly the main cause of eutrophication. This undesirable process can severely affect many aquatic biotas in the world. More management practices are proposed but long-term monitoring of phosphorus level is necessary to ensure that the eutrophication won't occur. Passive sampling techniques, which have been developed over the last decades, could provide several advantages to the conventional sampling methods including simpler sampling devices, more cost-effective sampling campaign, providing flow proportional load as well as representative average of concentrations of phosphorus in the environment. Although some types of passive samplers are commercially available, their uses are still scarcely reported in the literature. In Japan, there is limited application of passive sampling technique to monitor phosphorus even in the field of agricultural environment. This paper aims to introduce the relatively new P-sampling techniques and their potential to use in environmental monitoring studies.

Applications of passive sampling techniques in monitoring organic pollutants in the environment

As there are a myriad of micro organic pollutants that can affect the well-being of human and other organisms in the environment the need for an effective monitoring tool is eminent. Passive sampling techniques, which have been developed over the last decades, could provide several advantages to the conventional sampling methods including simpler sampling devices, more cost-effective sampling campaign, providing time-integrated load as well as representative average of concentrations of pollutants in the environment. Those techniques have been applied to monitor many pollutants caused by agricultural activities, i.e. residues of pesticides, veterinary drugs and so on. Several types of passive samplers are commercially available and their uses are widely accepted. However, not many applications of those techniques have been found in Japan, especially in the field of agricultural environment. This paper aims to introduce the field of passive sampling and then to describe some applications of passive sampling techniques in environmental monitoring studies related to the agriculture industry.