Video segmentation with superpixels

Due to its importance, video segmentation has regained interest recently. However, there is no common agreement about the necessary ingredients for best performance. This work contributes a thorough analysis of various within- and between-frame affinities suitable for video segmentation. Our results show that a frame-based superpixel segmentation combined with a few motion and appearance-based affinities are sufficient to obtain good video segmentation performance. A second contribution of the paper is the extension of [1] to include motion-cues, which makes the algorithm globally aware of motion, thus improving its performance for video sequences. Finally, we contribute an extension of an established image segmentation benchmark [1] to videos, allowing coarse-to-fine video segmentations and multiple human annotations. Our results are tested on BMDS [2], and compared to existing methods. © 2013 Springer-Verlag.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

Phylogenetic relationships among the genera of the Penaeidae (Crustacea : Decapoda) revealed by mitochondrial 16S rRNA gene sequences

The phylogenetic relationships within the family Penaeidae are examined based on mitochondrial 16S rRNA gene sequence analysis of 30 species from 20 genera. The analysis generally supports the three- tribe scheme proposed by Burkenroad ( 1983) but it is not consistent with the five- group classification of Kubo ( 1949). Three clades are resolved: ( Penaeus sensu stricto + Fenneropenaeus + Litopenaeus + Farfantepenaeus + Marsupenaeus + Melicertus + Funchalia + Heteropenaeus), ( Metapenaeus + Parapenaeopsis + Xiphopenaeus + Rimapenaeus + Megokris + Trachysalambria) and ( Metapenaeopsis + Penaeopsis + Parapenaeus), corresponding to the Penaeini, Trachypenaeini and Parapenaeini respectively, while the affinities of Atypopenaeus and Trachypenaeopsis are obscure. The molecular data support that Miyadiella represents the juvenile stage of Atypopenaeus. Within the Trachypenaeini, Trachypenaeus sensu lato is clearly paraphyletic, while the monophyly of Penaeus sensu lato in the Penaeini is questionable.

Effects of CO2 enrichment on the bloom-forming cyanobacterium Microcystis aeruginosa (Cyanophyceae): Physiological responses and relationships with the availability of dissolved inorganic carbon

Microcystis aeruginosa Kutz. 7820 was cultured at 350 and 700 muL.L-1 CO2 to assess the impacts of doubled atmospheric CO2 concentration on this bloom-forming cyanobacterium. Doubling Of CO2 concentration in the airflow enhanced its growth by 52%-77%, with pH values decreased and dissolved inorganic carbon (DIC) increased in the medium. Photosynthetic efficiencies and dark respiratory rates expressed per unit chl a tended to increase with the doubling of CO2. However, saturating irradiances for photosynthesis and light-saturated photosynthetic rates normalized to cell number tended to decrease with the increase of DIC in the medium. Doubling of CO2 concentration in the airflow had less effect on DIC-saturated photosynthetic rates and apparent photosynthetic affinities for DIC. In the exponential phase, CO2 and HCO3- levels in the medium were higher than those required to saturate photosynthesis. Cultures with surface aeration were DIC limited in the stationary phase. The rate of CO2 dissolution into the liquid increased proportionally when CO2 in air was raised from 350 to 700 muL.L-1, thus increasing the availability of DIC in the medium and enhancing the rate of photosynthesis. Doubled CO2 could enhance CO2 dissolution, lower pH values, and influence the ionization fractions of various DIC species even when the photosynthesis was not DIC limited. Consequently, HCO3- concentrations in cultures were significantly higher than in controls, and the photosynthetic energy cost for the operation of CO2 concentrating mechanism might decrease.

Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background: Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results: To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/ 21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion: Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

Integrated lectin affinity microfluidic chip for glycoform separation

Lectin affinity chromatography was miniaturized into a microfluidic format, which results in improvement of performance, as compared to the conventional method. A lectin affinity monolith column was prepared in the microchannel of a microfluidic chip. The porous monolith was fabricated by UV-initiated polymerization of ethylene dimethacrylate (EDMA) and glycidyl methacrylate (GMA) in the presence of porogeneities, followed by immobilization of pisum sativum agglutinin (PSA) on the monolith matrix. Using electroosmosis as the driven force, lectin affinity chromatographies of three kinds of glycoprotein, turkey ovalbumin (TO), chicken ovalbumin (CO), and ovomucoid (OM), were carried out on the microfluidic system. All the glycoproteins were successfully separated into several fractions with different affinities toward the immobilized PSA. The integrated system reduces the time required for the lectin affinity chromatography reaction to similar to3%, thus, the overall analysis time from 4 h to 400 s. Only 300 pg of glycoprotein is required for the whole separation process. Moreover, troublesome operations for lectin affinity chromatography are simplified.

Influence of drying method on morphology and properties of asymmetric cellulose hollow fiber membrane

Using a dry/wet spinning process, asymmetric cellulose hollow fiber membranes (CHFM) were prepared from a dope composed of cellulose/N-methylmorpholine-N-oxide/water. The formation mechanism for the finger-like macrovoids at the inner portion of as-spun fibers was explained. Naturally drying and three solvent exchange drying methods were tried to investigate their influence on morphology and properties of CHFM. It was found that the ethanol-hexane exchange drying was an appropriate method to minimize morphology change of the as-spun CHFM, whereas the naturally drying caused the greatest shrinkage of the fibers that made the porous membrane become dense. The result, CHFM from ethanol-hexane exchange drying performed the highest gas permeation rate but gas permeation of the naturally dried membrane could not be detectable. The resultant CHFM from the ethanol-hexane exchange drying also showed acceptable, mechanical properties, thus it was proposed to be an appropriate method for gas separation purpose. The experimental results supported the proposed drying mechanism of CHFM. The free water would evaporate or be replaced by a solvent that subsequently would evaporate but the bonded water would remain in the membrane. What dominated the changes of membrane morphology during drying should be. the molecular affinities of cellulose-water, water-solvent and solvent-solvent. (C) 2004 Elsevier B.V. All rights reserved.

Sorption of metals on humic acid

The sorption on humic acid (HA) of metals from an aqueous solution containing Hg(II). Fe(III), Pb, Cu, Al, Ni, Cr(III), Cd, Zn, Co and Mn, was investigated with special emphasis on effects of pH, metal concentration and HA concentration. The sorption efficiency tended to increase with rise in pH, decrease in metal concentration and increase in HA concentration of the equilibrating solution. At pH 2.4. the order of sorption was: Hg Fe Pb Cu=Al Ni Cr=Zn=Cd=Co=Mn. At pH 3.7. the order was: Hg and Fe were always most readily removed, while Co and Mn were sorbed least readily. There were indications of competition for active sites (CO2H and phenolic OH groups) on the HA between the different metals. We were unable to find correlations between the affinities of the eleven metals to sorb on HA and their atomic weights, atomic numbers, valencies, and crystal and hydrated ionic radii. The sorption of the eleven metals on the HA could be described by the equation Full-size image (1K), where Y = % metal removed by HA; X = mgHA; and A and B are empirical constants

Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry

In this study, electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding interactions of ten flavonoid aglycones and ten flavonoid glycosides with DNA duplexes. Relative binding affinities of the flavonoids toward DNA duplexes were estimated based on the fraction of bound DNA. The results revealed that the 4'-OH group of flavonoid aglycones was essential for their DNA-binding properties. Flavonoid glycosides with sugar chain linked on ring A or ring B showed enhanced binding toward the duplexes over their aglycone counterparts, whereas glycosylation of the flavonol quercetin on ring C exhibited a less pronounced effect.

Studies on alkaloids binding to GC-rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode.

Reducing HAuCl4 by the C-60 dianion: C-60-directed self-assembly of gold nanoparticles into novel fullerene bound gold nanoassemblies

The C-60 dianion is used to reduce tetrachloroauric acid (HAuCl4) for the first time; three-dimensional C-60 bound gold (Au-C-60) nanoclusters are obtained from C-60-directed self-assembly of gold nanoparticles due to the strong affinities of Au-C-60 and C-60-C-60. The process was monitored in situ by UV-vis-NIR spectroscopy. The resulting Au-C-60 nanoclusters were characterized using transmission electron microscopy (TEM), selected area electron diffraction (SAED), energy-dispersive spectroscopy (EDS), x-ray powder diffraction (XRD), x-ray photoelectron spectroscopy (XPS), and FT-IR and Raman spectroscopies.

Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV-vis, fluorescence, circular dichroism (CD) spectroscopy, UV-rnelting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation.

Injection, Transport, Absorption and Phosphorescence Properties of a Series of Blue-Emitting Ir(III) Emitters in OLEDs: a DFT and Time-Dependent DFT Study

Quantum-chemistry methods were explored to investigate the electronic structures, injection and transport properties, absorption and phosphorescence mechanism of a series of blue-emitting Ir(III) complexes {[(F-2-ppy)(2)Ir(pta -X/pyN4)], where F-2-ppy = (2,4-difluoro)phenylpyridine; pta = pyridine-1,2,4-triazole; X = phenyl(1); p-tolyl (2); 2,6-difluororophenyl (3); -CF3 (4), and pyN4 = pyridine-1,2,4-tetrazolate (5)}, which are used as emitters in organic light-emitting diodes (OLEDs). The mobility of hole and electron were studied computationally based on the Marcus theory. Calculations of Ionization potentials (IPs) and electron affinities (EAs) were used to evaluate the injection abilities of holes and electrons into these complexes.

Theoretical studies on electronic structures, spectra and charge transporting properties of a series of Pt((CN)-N-Lambda)(2) complexes

We report a quantum-chemical study of electronic, optical and charge transporting properties of four platinum (II) complexes, pt((CN)-N-Lambda)(2) ((CN)-N-Lambda=phenylpyridine or thiophenepyridine). The lowest-lying absorptions at 442, 440, 447 and 429 nm are all attributed to the mixed transition characters of metal-to-ligand charge transfer (MLCT) and ligand-centered (LC) pi - pi(*) transition. While, unexpectedly, the lowest-lying phosphorescent emissions at 663, 660, 675 and 742 nm are mainly from metal-to-ligand charge transfer ((MLCT)-M-3) ligand-centered (LC) pi ->pi* transition. Ionization potential (IP), electron affinities (EA) and reorganization energy P (lambda(hole/electron)) were obtained to evaluate the charge transfer and balance properties between hole and electron.

Chemical Bonding and Electronic Structure of 4d-Metal Monosulfides

Bond distances, vibrational frequencies, dissociation energies, electron affinities, ionization potentials and dipole moments of the title molecules in neutral and charged ions were studied by use of density functional method. Ground states for each molecule were assigned. The calculated bond distance decreases with the increasing of atomic number of 4d metals, reaches minimum at RhS, then increases. For cationic molecules, the calculated bond distance decreases to the minimum at MoS+, then increases. The calculated vibrational frequency decreases from YS(YS+) to PdS(PdS+) for both neutral and cationic molecules. The bond ionic character decreases from YS(YS+) to PdS(PdS+) for neutral and cationic molecules. The bonding patterns are discussed and compared with the available studies.