Deeper and wider fully convolutional network coupled with conditional random fields for scene labeling

Deep convolutional neural networks (DCNNs) have been employed in many computer vision tasks with great success due to their robustness in feature learning. One of the advantages of DCNNs is their representation robustness to object locations, which is useful for object recognition tasks. However, this also discards spatial information, which is useful when dealing with topological information of the image (e.g. scene labeling, face recognition). In this paper, we propose a deeper and wider network architecture to tackle the scene labeling task. The depth is achieved by incorporating predictions from multiple early layers of the DCNN. The width is achieved by combining multiple outputs of the network. We then further refine the parsing task by adopting graphical models (GMs) as a post-processing step to incorporate spatial and contextual information into the network. The new strategy for a deeper, wider convolutional network coupled with graphical models has shown promising results on the PASCAL-Context dataset.

Effect of lipopolysaccharide on alteration of phospholipids and their fatty acid composition in spleen and thymus by in vitro metabolic labeling

Lipopolysaccharide (LPS) is an endotoxin, a potent stimulator of immune response and induction of LPS leads to acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). ARDS is a life-threatening disease worldwide with a high mortality rate. The immunological effect of LPS with spleen and thymus is well documented; however the impact on membrane phospholipid during endotoxemia has not yet been studied. Hence we aimed to investigate the influence of LPS on spleen and thymus phospholipid and fatty acid composition by 32P]orthophosphate labeling in rats. The in vitro labeling was carried out with phosphate-free medium (saline). Time course, LPS concentration-dependent, pre- and post-labeling with LPS and fatty acid analysis of phospholipid were performed. Labeling studies showed that 50 mu g LPS specifically altered the major phospholipids, phosphatidylcholine and phosphatidylglycerol in spleen and phosphatidylcholine in thymus. Fatty acid analysis showed a marked alteration of unsaturated fatty acids/saturated fatty acids in spleen and thymus leading to immune impairment via the fatty acid remodeling pathway. Our present in vitro lipid metabolic labeling study could open up new vistas for exploring LPS-induced immune impairment in spleen and thymus, as well as the underlying mechanism.

Cluster labeling for multilingual scatter/gather using comparable corpora

Scatter/Gather systems are increasingly becoming useful in browsing document corpora. Usability of the present-day systems are restricted to monolingual corpora, and their methods for clustering and labeling do not easily extend to the multilingual setting, especially in the absence of dictionaries/machine translation. In this paper, we study the cluster labeling problem for multilingual corpora in the absence of machine translation, but using comparable corpora. Using a variational approach, we show that multilingual topic models can effectively handle the cluster labeling problem, which in turn allows us to design a novel Scatter/Gather system ShoBha. Experimental results on three datasets, namely the Canadian Hansards corpus, the entire overlapping Wikipedia of English, Hindi and Bengali articles, and a trilingual news corpus containing 41,000 articles, confirm the utility of the proposed system.

Differential binding of ppGpp and pppGpp to E-coli RNA polymerase: photo-labeling and mass spectral studies

(p) ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the beta-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of beta'/omega-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra-and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on beta'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the beta-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the beta'-subunit. However, we were unable to identify any binding site of pppGpp on the beta-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.

Application of methyl parathion hydrolase (MPH) as a labeling enzyme

Methyl parathion hydrolase (MPH) is an enzyme that catalyzes the degradation of methyl parathion, generating a yellow product with specific absorption at 405 nm. The application of MPH as a new labeling enzyme was illustrated in this study. The key advantages of using MPH as a labeling enzyme are as follows: (1) unlike alkaline phosphatase (AP), horseradish peroxidase (HRP), and glucose oxidase (GOD), MPH is rarely found in animal cells, and it therefore produces less background noise; (2) its active form in solution is the monomer, with a molecular weight of 37 kDa; (3) its turnover number is 114.70 +/- 13.19 s(-1), which is sufficiently high to yield a significant signal for sensitive detection; and (4) its 3D structure is known and its C-terminal that is exposed to the surface can be easily subjected to the construction of genetic engineering monocloning antibody-enzyme fusion for enzyme-linked immunosorbent assay (ELISA). To demonstrate its utility, MPH was ligated to an single-chain variable fragment (scFv), known as A1E, against a white spot syndrome virus (WSSV) with the insertion of a [-(Gly-Ser)(5)-] linker peptide. The resulting fusion protein MPH-A1E possessed both the binding specificity of the scFv segment and the catalytic activity of the MPH segment. When MPH-A1E was used as an ELISA reagent, 25 ng purified WSSV was detected; this was similar to the detection sensitivity obtained using A1E scFv and the HRP/Anti-E Tag Conjugate protocol. The fusion protein also recognized the WSSV in 1 mu L hemolymph from an infected shrimp and differentiated it from a healthy shrimp.

tilt menu: using the 3d orientation information of pen devices to extend the selection capability of pen-based user interfaces

We present a new technique called‘Tilt Menu’ for better extending selection capabilities of pen-based interfaces.The Tilt Menu is implemented by using 3D orientation information of pen devices while performing selection tasks.The Tilt Menu has the potential to aid traditional onehanded techniques as it simultaneously generates the secondary input (e.g., a command or parameter selection) while drawing/interacting with a pen tip without having to use the second hand or another device. We conduct two experiments to explore the performance of the Tilt Menu. In the first experiment, we analyze the effect of parameters of the Tilt Menu, such as the menu size and orientation of the item, on its usability. Results of the first experiment suggest some design guidelines for the Tilt Menu. In the second experiment, the Tilt Menu is compared to two types of techniques while performing connect-the-dot tasks using freeform drawing mechanism. Results of the second experiment show that the Tilt Menu perform better in comparison to the Tool Palette, and is as good as the Toolglass.

Development of functionalized terbium fluorescent nanoparticles for antibody labeling and time-resolved fluoroimmunoassay application

Silica-based functionalized terbium fluorescent nanoparticles were prepared, characterized and developed as a fluorescence probe for antibody labeling and time-resolved fluoroimmunoassay. The nanoparticles were prepared in a water-in-oil (W/O) microemulsion containing a strongly fluorescent Tb3+ chelate. N,N.N-1,N-1-12,6-bis(3'-aminomethyl-1'-pyrazolyl)phenylpyridine] tetrakis(acetate)-Tb3+ (BPTA-Tb3+), Triton X-100, octanol, and cyclohexane by controlling copolymerization of tetraethyl orthosilicate (TEOS) and 3-[2-(2- aminoethylamino)-ethylamino]propyl-trimethoxysilane (AEPS) with ammonia water. The characterizations by transmission electron microscopy and fluorometric quantum methods show that the nanoparticles are spherical and uniform in size, 45 +/- 3 nm in diameter, strongly fluorescent with fluorescence yield of 10% and a long fluorescence lifetime of 2.0 ms. The amino groups directly introduced to the nanoparticle's surface by using AEPS in the preparation made the surface modification and bioconjugation of the nanoparticles easier. The nanoparticle-labeled anti-human alpha-fetoprotein antibody was prepared and used for time-resolved fluoroimmunoassay of (x-fetoprotein (AFP) in human serum samples. The assay response is linear from 0.10 ng ml(-1) to about 100 ng ml(-1) with the detection limit of 0.10 ng ml(-1). The coefficient variations (CVs) of the method are less than 9.0%. and the recoveries are in the range of 84-98% for human serum sample measurements. (C) 2004 Elsevier B.V. All rights reserved.

[Ru(bpy)(2)(dcbpy)NHS] Labeling/Aptamer-Based Biosensor for the Detection of Lysozyme by Increasing Sensitivity with Gold Nanoparticle Amplification

A novel [Ru(bpy)(2) (dcbpy)NHS] labeling/aptamer-based biosensor combined with gold nanoparticle amplification for the determination of lysozyme with an electrochemiluminescence (ECL) method is presented. In this work, an aptamer, an ECL probe, gold nanoparticle amplification, and competition assay are the main protocols employed in ECL detection. With all the protocols used, an original biosensor coupled with an aptamer and [Ru(bpy)(2)(dcbpy)NHS] has been prepared. Its high selectivity and sensitivity are the main advantages over other traditional [Ru(bpy)(3)](2+) biosensors. The electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) characterization illustrate that this biosensor is fabricated successfully. Finally, the biosensor was applied to a displacement assay in different concentrations of lysozyme solution, and an ultrasensitive ECL signal was obtained. The ECL intensity decreased proportionally to the lysozyme concentration over the range 1.0 x 10-(13)-1.0 x 10(-8) mol L-1 with a detection limit of 1.0 x 10(-13) mol L-1.

Europium ion labeling anti-HBs

A microsecond time-resolved laser fluorescence spectroscopic analysis set was developed, A chelate-cyclic anhydride of diethylenetrimin pentaacetic acid anhydride (DTPAA) was synthesized. An anti-HBs antibody was purified, A EU3+ -DTPAA-anti-HBs label was prepared by two step procedure. We described the optimal condtion with EU3+ as marker and DTPAA as chelate bounding to antibody molecule. Labeling parameters such as solvent pH, protein and chelate molar ratio, reaction time, separation method were discussed in detail.