Dictionary learning and sparse coding on Grassmann manifolds : an extrinsic solution

Recent advances in computer vision and machine learning suggest that a wide range of problems can be addressed more appropriately by considering non-Euclidean geometry. In this paper we explore sparse dictionary learning over the space of linear subspaces, which form Riemannian structures known as Grassmann manifolds. To this end, we propose to embed Grassmann manifolds into the space of symmetric matrices by an isometric mapping, which enables us to devise a closed-form solution for updating a Grassmann dictionary, atom by atom. Furthermore, to handle non-linearity in data, we propose a kernelised version of the dictionary learning algorithm. Experiments on several classification tasks (face recognition, action recognition, dynamic texture classification) show that the proposed approach achieves considerable improvements in discrimination accuracy, in comparison to state-of-the-art methods such as kernelised Affine Hull Method and graph-embedding Grassmann discriminant analysis.

The collision induced loss of carbon monoxide from deprotonated benzyl benzoate in the gas phase. An anionic 1,2-Wittig type rearrangement

The ion PhCO2--CHPh, upon collision activation, undergoes competitive losses of CO and CO2 of which the former process produces the base peak of the spectrum. Product ion and substituent effect (Hammett) studies indicate that PhCO2--CHPh cyclises to a deprotonated hydroxydiphenyloxirane which ring opens to PhCOCH(O-)Ph. This anion then undergoes an anionic 1,2-Wittig type rearrangement {through [PhCO- (PhCHO)]} to form Ph2CHO- and CO. The mechanism of the 1,2-rearrangement has been probed by an ab initio study [at MP4(SDTQ)/6-31++G(d,p) level] of the model system HCOCH2O- →; MeO- + CO The analogous system RCO2--CHPh (R = alkyl) similarly loses CO, and the migratory aptitudes of the alkyl R groups in this reaction are Bu′ > Me > Et ∼Pri). This trend correlates with the order of anion basicities (i.e. the order of ΔG○acid values of RH), supporting the operation of an anion migration process. The loss of CO2 from PhCO2--CHPh yields Ph2CH- as the anionic product: several mechanistic scenarios are possible, one of which involves an initial ipso nucleophilic substitution.

The loss of CO from the ortho, meta and para forms of deprotonated methyl benzoate in the gas phase

The ortho, meta and para anions of methyl benzoate may be made in the source of a mass spectrometer by the S(N)2(Si) reactions between HO- and methyl (o-, m-, and p-trimethylsilyl)benzoate respectively. All three anions lose CO upon collisional activation to form the ortho anion of anisole in the ratio ortho>>meta > para. The rearrangement process is charge directed through the ortho anion. Theoretical calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that the conversion of the meta and para anions to the ortho anion prior to loss of CO involve 1,2-H transfer(s), rather than carbon scrambling of the methoxycarbonylphenyl anion. There are two mechanisms which can account for this rearrangement, viz. (A) cyclisation of the ortho anion centre to the carbonyl group of the ester to give a cyclic carbonyl system in which the incipient methoxide anion substitutes at one of the two equivalent ring carbons of the three membered ring to yield an intermediate which loses CO to give the ortho anion of anisole, and (B) an elimination reaction to give an intermediate benzyne-methoxycarbonyl anion complex in which the MeOCO- species acts as a MeO- donor, which then adds to benzyne to yield the ortho anion of anisole. Calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that (i) the barrier in the first step (the rate determining step) of process A is 87 kJ mol(-1) less than that for the synchronous benzyne process B, and (ii) there are more low frequency vibrations in the transition state for benzyne process B than for the corresponding transition state for process A. Stepwise process A has the lower barrier for the rate determining step, and the lower Arrhenius factor: we cannot differentiate between these two mechanisms on available evidence.

Concerted HO2 elimination from alpha-Aminoalkylperoxyl free radicals : Experimental and theoretical evidence from the gas phase NH2 center dot CHCO2- + O-2 reaction

We have investigated the gas-phase reaction of the alpha-aminoacetate (glycyl) radical anion (NH2(sic)CHCO2-) with O-2 using ion trap mass spectrometry, quantum chemistry, and statistical reaction rate theory. This radical is found to undergo a remarkably rapid reaction with O-2 to form the hydroperoxyl radical (HO2(sic)) and an even-electron imine (NHCHCO2-), with experiments and master equation simulations revealing that reaction proceeds at the ion molecule collision rate. This reaction is facilitated by a low-energy concerted HO2(sic) elimination mechanism in the NH2CH(OO(sic))CO2- peroxyl radical. These findings can explain the widely observed free-radical-mediated oxidation of simple amino acids to amides plus alpha-keto acids (their imine hydrolysis products). This work also suggests that imines will be the main intermediates in the atmospheric oxidation of primary and secondary amines, including amine carbon capture solvents such as 2-aminoethanol (commonly known as monoethanolamine, or MEA), in a process that avoids the ozone-promoting conversion of (sic)NO to (sic)NO2 commonly encountered in peroxyl radical chemistry.

Direct observation of the gas phase reaction of the cyclohexyl radical with dioxygen using a distonic radical ion approach

Alkylperoxyl radicals are intermediates in the oxidation Of hydrocarbons. The reactive nature of these intermediates, however, has made therin elusive to direct observation and isolation. We have employed ion trap mass spectrometry to synthesize and characterize 4-carboxylatocyclohexyl radical anions ((center dot)C(6)H(10)-CO(2)(-)) and observe their reactivity in the presence of dioxygen. The resulting reaction is facile (k = 1.8 x 10(-10) cm(3) molecule(-1) s(-1) or 30% of calculated collision rate) and results in (i) the addition Of O(2) to form stabilized 4-carboxylatocyclohexylperoxyl radical anions ((center dot)OO-C(6)H(10)-CO(2)(-)), providing the first direct observation of a cyclohexylperoxyl radical, and (ii) elimination of HO(2)(center dot) and HO(center dot) radicals consistent with recent laser-induced fluorescence studies of the reaction of neutral cyclohexyl radicals with O(2). Electronic structure calculations at the B3LYP/6-31+G(d) level of theory reveal viable pathways for the observed reactions showing that formation of the peroxyl radical is exothermic by 37 kcal mol(-1) with subsequent transition states its low as -6.6 kcal mol(-1) (formation of HO(2)(center dot)) and -9.1 kcal mol(-1) (formation of HO(center dot)) with respect to the entrance channel. The combined computational and experimental data Suggest that the structures of the reaction products correspond to cyclohexenes and epoxides from HO(2)(center dot) and HO(center dot) loss, respectively, while alternative pathways leading to cyclohexanone or ring-opened isomers ate not observed, Activation of the charged peroxyl radical (center dot)OO-C(6)H(10)-CO(2)(-) by collision induced disassociation also results in the loss Of HO(2)(center dot) and HO(center dot) radicals confirming that these products are directly connected to the peroxyl radical intermediate.

Supernatants of acquired immunodeficiency syndrome-related Kaposi's sarcoma cells induce endothelial cell chemotaxis and invasiveness

Kaposi's sarcoma (KS) in general, and acquired immunodeficiency syndrome-related KS (AIDS-KS) in particular, is a highly invasive and intensely angiogenic neoplasm of unknown cellular origin. We have recently established AIDS-KS cells in long term culture and reported the development of KS-like lesions in nude mice inoculated with these cells. Here, we have examined the in vitro invasiveness of basement membrane by AIDS-KS cells, as well as the effect(s) of their supernatants on the migration and invasiveness of human vascular endothelial cells. AIDS-KS cells were highly invasive in the Boyden chamber invasion assay and formed invasive, branching colonies in a 3-dimensional gel (Matrigel). Normal endothelial cells form tube-like structures on Matrigel. AIDS-KS cell-conditioned media induced endothelial cells to form invasive clusters in addition to tubes. KS-cell-conditioned media, when placed in the lower compartment of the Boyden chamber, stimulated the migration of human and bovine vascular endothelial cells across filters coated with either small amounts of collagen IV (chemotaxis) or a Matrigel barrier (invasion). Basic fibroblast growth factor could also induce endothelial cell chemotaxis and invasion in these assays. However, when antibodies to basic fibroblast growth factor were used the invasive activity induced by the AIDS-KS-cell-conditioned media was only marginally inhibited, suggesting that the large quantities of basic fibroblast growth factor-like material released by the AIDS-KS cells are not the main mediators of this effect. Specific inhibitors of laminin and collagenase IV action, which represent critical determinants of basement membrane invasion, blocked the invasiveness of the AIDS-KS cell-activated endothelial cells in these assays. These data indicate that KS cells appear to be of smooth muscle origin but secrete a potent inducer of endothelial cell chemotaxis and invasiveness which could be responsible for angiogenesis and the resulting highly vascularized lesions. These assays appear to be a model to study the invasive spread and angiogenic capacity of human AIDS-related KS and should prove useful in the identification of molecular mediators and potential inhibitors of neoplastic neovascularization.

Securing medical devices Part B : what’s available for nasogastric tubes?

This article is the second part of a two-part series examining securement options for commonly used therapeutic devices in the adult intensive care unit. Part A focused on endotracheal device securement.1 This article addresses nasogastric tube (NGT) securement options and with the aim of identifying the available range of NGT securement devices in Australia as a resource for clinicians seeking to explore options for tube stabilisation. Nasogastric feeding or gastric decompression tubes are commonly inserted via the nostril/nares. The National Pressure Ulcer Advisory Panel (NPUAP) 2011 position statement on mucosal pressure injuries, highlighted that mucosal tissues are vulnerable to pressure from devices.2 Securing of these devices sometimes leads to pressure-related injury to the internal mucosa due to difficulty visualising the mucosa and failure to reposition the nasogastric tube to relieve the pressure in a particular area.3 The nasal orifice is much smaller than the oral cavity and regular tube position changes are vital to minimise the risk of mucosal damage and ulcer development.

Anionic migration in aromatic systems effected by collisional activation. Unusual fragmentations of deprotonated anilides containing methoxyl and ethoxyl substituents

Long-range cross-ring reactions occur when (M - H)(-) ions of methoxy- and ethoxy-C6H4-(-)NCOR (R = H, CH3, C6H5 and CH3O) are subjected to collisional activation, These reactions are generally minor processes: a particular example is the cross-ring elimination p-C2H5O-C6H4-(NCOCH3)-N-- --> [CH3-(p-C2H5O-C6H4-NCO)] --> p-(O--)-C6H4-NCO + C2H4 + CH4. Major processes of these (M - H)(-) ions involve (i) losses of radicals to form stabilised radical anions, e.g. (a) loss of a ring H-. or (b) CH3. (or C2H5.) from the alkoxy group, and (ii) proximity effects when the two substituents are ortho, e.g. loss of CH3OH from o-CH3O-C6H4-(NCHO)-N-- yields deprotonated benzoxazole. Another fragmentation of an arylmethoxyl anion involves loss of CH2O. It is proposed that losses of CH2O are initiated by anionic centres but the actual mechanisms in the cases studied depend upon the substitution pattern of the methoxyanilide: o- and p-methoxyanilides may undergo ipso proton transfer/elimination reactions, whereas the in-analogues undergo proton transfer reactions to yield an o-CH3O substituted aryl carbanion followed by proton transfer from CH3O to the carbanion site with concomitant loss of CH2O.

Binding and degradation of hyaluronan by human breast cancer cell lines expressing different forms of CD44 : correlation with invasive potential

In the present study, we examined a panel of human breast cancer cell lines with regard to their expression of CD44 and ability to bind and degrade hyaluronan. The cell lines expressed varying amounts of different molecular weight forms of CD44 (85-200 kDa) and, in general, those that expressed the greatest amounts of CD44 were the most invasive as judged by in vitro assays. In addition, the ability to bind and degrade hyaluronan was restricted to the cell lines expressing high levels of CD44, and both these functions were blocked by an antibody to CD44 (Hermes-1). Moreover, the rate of [3H]hyaluronan degradation was highly correlated with the amount of CD44 (r = 0.951, P < 0.0001), as well as with the invasive potential of the cells. Scatchard analysis of the [3H]hyaluronan binding of these cells revealed the existence of significant differences in both their binding capacity and their dissociation constant. To determine the source of this deviation, the different molecular weight forms of CD44 were partially separated by gel filtration chromatography. In all cell lines, the 85 kDa form was able to bind hyaluronan, although with different affinities. In contrast, not all of the high molecular weight forms of CD44 had this ability. These results illustrate the diversity of CD44 molecules in invasive tumor cells, and suggest that one of their major functions is to degrade hyaluronan.

Synthesis and characterization of titanium sol–gels in varied gravity

Two unique test systems were designed and built to allow the effects of varied gravity (high, normal, reduced) during synthesis of titanium sol–gels to be studied. A centrifuge capable of providing high gravity environments of up to 70 g for extended periods while applying a 100 mbar vacuum and a temperature of 40–50 °C to the reaction chambers was developed. The second system was used in the QUT Microgravity Drop Tower Facility also provided the same thermal and vacuum conditions used in the centrifuge, but was required to operate autonomously during free fall. Through the use of post synthesis instrumental characterization, it was found that increased gravity levels during synthesis, had the greatest effect on the final products. Samples produced in reduced and normal gravity appeared to form amorphous gels containing very small particles with moderate surface areas. Whereas crystalline anatase (TiO2), was found to form in samples synthesized above 5 g with significant increases in crystallinity, particle size and surface area observed when samples were produced at gravity levels up to 70 g. It is proposed that for samples produced in higher gravity, an increased concentration gradient of water is forms at the bottom of the reacting film due to forced convection. The particles formed in higher gravity diffuse downward toward this excess of water, which favors the condensation reaction of remaining sol–gel precursors with the particles promoting increased particle growth. Due to the removal of downward convection in reduced gravity, particle growth due to condensation reaction processes are physically hindered hydrolysis reactions favored instead. Another significant finding from this work was that anatase could be produced at relatively low temperatures of 40–50 °C instead of the conventional method of calcination above 450 °C solely through sol–gel synthesis at higher gravity levels.

Progression of human breast cancer cells from hormone-dependent to hormone-independent growth both in vitro and in vivo

We have isolated a series of sublines of the hormone-dependent MCF-7 human breast cancer cell line after selection both in vivo and in vitro for growth in the presence of subphysiological concentrations of estrogens. These sublines represent a model system for study of the processes leading to hormonal autonomy. The cells form growing tumors in ovariectomized athymic nude mice in the absence of estrogen supplementation but retain some responsivity to estrogen as determined by stimulation of the rate of tumor growth in vivo and by induction of progesterone receptor. An ovarian-independent but hormone-responsive phenotype may occur early in the natural progression to hormone-independent and unresponsive growth in breast cancer. We observed no change in the affinity or decrease in the level of expression of estrogen receptors and progesterone receptors among the sublines and the parental cells. Epidermal growth factor receptors are not overexpressed in ovarian-independent cells. Thus, altered hormone receptor expression may be a late event in the acquisition of a hormone-independent and unresponsive phenotype. Sublines isolated by in vivo but not in vitro selection are more invasive than the parental cells both in vivo and across an artificial basement membrane in vitro. Thus, as yet unknown tumor-host interactions may be important in the development of an invasive phenotype. Furthermore, acquisition of the ovarian-independent and invasive phenotypes can occur independently.

Gelatinase A (MMP-2) activation by skin fibroblasts : dependence on MT1-MMP expression and fibrillar collagen form

The respective requirements of collagen and MT1-MMP in the activation of MMP-2 by primary fibroblast cultures were explored further. Three-dimensional gels enriched in human collagen types I and III or composed of recombinant human type II or III collagen, caused increased MT1-MMP production (mRNA and protein) and induced MMP-2 activation. Only marginal induction was seen with dried monomeric collagen confirming the need for collagen fibrillar organisation for activation. To our surprise, relatively low amounts (as low as 25 μg/ml) of acid soluble type I collagen added to fibroblast cultures also induced potent MMP-2 activation. However, the requirement for collagen fibril formation by the added collagen was indicated by the inhibition seen when the collagen was pre-incubated with a fibril-blocking peptide, and the reduced activation seen with alkali-treated collagen preparations known to have impaired fibrilisation. Pre-treatment of the collagen with sodium periodate also abrogated MMP-2 activation induction. Further evidence of the requirement for collagen fibril formation was provided by the lack of activation when type IV collagen, which does not form collagen fibrils, was added in the cultures. Fibroblasts derived from MT1-MMP-deficient mice were unable to activate MMP-2 in response to either three-dimensional collagen gel or added collagen solutions, compared to their littermate controls. Collectively, these data indicate that the fibrillar structure of collagen and MT1-MMP are essential for the MMP-2 activational response in fibroblasts.

Accurately defining the reference condition for summary biotic metrics: A comparison of four approaches

Protocols for bioassessment often relate changes in summary metrics that describe aspects of biotic assemblage structure and function to environmental stress. Biotic assessment using multimetric indices now forms the basis for setting regulatory standards for stream quality and a range of other goals related to water resource management in the USA and elsewhere. Biotic metrics are typically interpreted with reference to the expected natural state to evaluate whether a site is degraded. It is critical that natural variation in biotic metrics along environmental gradients is adequately accounted for, in order to quantify human disturbance-induced change. A common approach used in the IBI is to examine scatter plots of variation in a given metric along a single stream size surrogate and a fit a line (drawn by eye) to form the upper bound, and hence define the maximum likely value of a given metric in a site of a given environmental characteristic (termed the 'maximum species richness line' - MSRL). In this paper we examine whether the use of a single environmental descriptor and the MSRL is appropriate for defining the reference condition for a biotic metric (fish species richness) and for detecting human disturbance gradients in rivers of south-eastern Queensland, Australia. We compare the accuracy and precision of the MSRL approach based on single environmental predictors, with three regression-based prediction methods (Simple Linear Regression, Generalised Linear Modelling and Regression Tree modelling) that use (either singly or in combination) a set of landscape and local scale environmental variables as predictors of species richness. We compared the frequency of classification errors from each method against set biocriteria and contrast the ability of each method to accurately reflect human disturbance gradients at a large set of test sites. The results of this study suggest that the MSRL based upon variation in a single environmental descriptor could not accurately predict species richness at minimally disturbed sites when compared with SLR's based on equivalent environmental variables. Regression-based modelling incorporating multiple environmental variables as predictors more accurately explained natural variation in species richness than did simple models using single environmental predictors. Prediction error arising from the MSRL was substantially higher than for the regression methods and led to an increased frequency of Type I errors (incorrectly classing a site as disturbed). We suggest that problems with the MSRL arise from the inherent scoring procedure used and that it is limited to predicting variation in the dependent variable along a single environmental gradient.