Comparative Proteomics Reveals Core vs. Unique Molecular Signatures for Dissimilatory Metal Reducing Bacteria Grown with Various Electron Acceptors

Dissimilatory metal reducing bacteria (DMRB) are probably one of the most respiratory versatile microorganisms on earth. Their ability to use metals as terminal electron acceptor allows them to survive in severe environments (e.g. radionuclide contaminated soil). In addition to metals, many other organic and inorganic substrates can be utilized as electron acceptors for DMRB respiration, including fumarate, nitrate, oxygen, etc. Genome information for many DMRB species is available, which reveals large numbers of c-type cytochrome encoding genes present in their genomes. For example, the genomes of three DMRBs, Anaeromyxobacter dehalogenans strain 2CP-C, Shewanella oneidensis strain MR-1, and Geobacter daltonii strain FRC-32, contain 69, 40, and 72 putative c-type cytochrome genes, respectively. Although mutagenesis techniques have determined the respiratory roles of several c-type cytochromes, gene disruption for majorities of the putative c-type cytochromes does not generate visible phenotypical alterations, and is not able to functionally link them to specific respirational activities. Thus, comprehensive proteome characterization for DMRBs is needed to elucidate the molecular mechanisms underlying their respirational versatilities. In this dissertation, a mass spectrometry-based proteomics approach was used to interrogate the proteomes of A. dehalogenans strain 2CP-C, S. oneidensis strain MR-1, and G. daltonii strain FRC-32. The proteomic responses of DMRBs to a wide range of electron acceptors were tested in this dissertation, including soluble and insoluble ferric iron, manganese oxide, fumarate, nitrate, oxygen, and nitrous oxide. The in-depth proteomic characterizations comparatively revealed the c-type cytochrome profiles of DMRBs, providing evidence for the identities and expressions of putative c-type cytochromes, and established the linkage between specific electron acceptor and individual c-type cytochromes. The entire proteome complements of DMRBs were also characterized, generating metabolic maps reflecting pathway-level activities responding to various electron acceptors. The results identified the core proteome carrying out the essential cellular machineries for each tested DMRB, and demonstrated clearly elevated energy metabolism for A. dehalogenans strain 2CP-C during respiration of metal electron acceptors. Comparative proteomics analysis between tested DMRB strains revealed the commonalities and differences of proteomic phenotypes displayed by different strains, and shed light into deeper understandings for DMRB metabolic activities

Stability and robustness of quasi-linear impulsive hybrid systems

AbstractBoth hybrid dynamical systems and impulsive dynamical systems are studied extensively in the literature. However, impulsive hybrid systems are not yet well studied. Nonetheless, many physical systems exhibit both system switching and impulsive jump phenomena. This paper investigates stability and robust stability of a class of quasi-linear impulsive hybrid systems by using the methods of Lyapunov functions and Riccati inequalities. Sufficient conditions for stability and robust stability of those systems are established. Some examples are given to illustrate the applicability of our results

Absolute stability of lurie systems with impulsive effects

AbstractThis paper studies absolute stability of Lurie systems with impulsive effects. Using the method of Lyapunov functions and the variation of parameters technique, we establish sufficient conditions for absolute stability

Low Resistivity Contrast Gas Bearing Formation Identification from Conventional Logs in Tight Gas Sandstones

It’s a great challenge in identifying gas bearing formation from conventional logs in tight gas sandstones due to the low resistivity contrast caused by high irreducible water saturation. Based on the difference of the principles of three kinds of porosity logs (density, neutron and acoustic logs), three porosities difference method, three porosities ratio method, correlation of neutron and density logs and the overlap method of water-filled porosity and total porosity are introduced to identify tight gas bearing reservoirs. In gas bearing formations, the difference of three porosities is higher than 0.0, the ratio of three porosities is higher than 1.0, the correlation between density and neutron logs is negative, and the water filled porosities are lower than total porosities. On the contrary, in water saturated formations, the difference of three porosities is lower than 0.0, the ratio of three porosities is lower than 1.0, the correlation between density and neutron logs is positive, and the water filled porosities are overlapped with total porosities. Considering the complexity of in-suit formation, when the proposed identification criterion are mainly meet, the pore fluid should be determined, field examples show that the proposed techniques are applicable in tight gas formation identification.Key words: Low resistivity contrast gas bearing formation; Tight gas sandstones;  Identification; Difference of three porosities; Ratio of three porosities; Correlation of neutron and density log

Discovery and Characterization of Circular and Chimeric RNAs in Complex Diseases

Non-co-linear RNAs, including circular and chimeric RNAs, have been investigated in a broad range of cellular processes and various diseases. The current biogenesis models of circular and chimeric RNAs depend on RNA splicing mechanisms. We hypothesized that some of the non-co-linear RNAs are products of an alternative mechanism other than RNA splicing. To test this hypothesis, we developed a method, which is independent of genome annotations and splicing signals, to identify Circular and Chimeric RNAs of All Types (C2AT or CAT for simplicity) by analyzing the RNA species profiled by whole genome RNA sequencing. Statistical analysis and experimental validation revealed that both circular RNAs (circRNAs) and chimeric RNAs may arise from the interior regions of exons and introns across the human genome, supporting a potential novel mechanism of biogenesis of circular and chimeric RNAs. Moreover, analysis of differential expressions of circRNAs and chimeric RNAs and their host genes suggested that these non-co-linear RNAs may play an important role in complex diseases, such as cancer and psoriasis. All the results from this systematic study of non-co-linear RNAs significantly expanded our understanding of the origin, diversity, and complexity of circRNAs and chimeric RNAs as well as their potential functions in complex diseases

Surface Defect Classification for Hot-Rolled Steel Strips by Selectively Dominant Local Binary Patterns

Developments in defect descriptors and computer vision-based algorithms for automatic optical inspection (AOI) allows for further development in image-based measurements. Defect classification is a vital part of an optical-imaging-based surface quality measuring instrument. The high-speed production rhythm of hot continuous rolling requires an ultra-rapid response to every component as well as algorithms in AOI instrument. In this paper, a simple, fast, yet robust texture descriptor, namely selectively dominant local binary patterns (SDLBPs), is proposed for defect classification. First, an intelligent searching algorithm with a quantitative thresholding mechanism is built to excavate the dominant non-uniform patterns (DNUPs). Second, two convertible schemes of pattern code mapping are developed for binary encoding of all uniform patterns and DNUPs. Third, feature extraction is carried out under SDLBP framework. Finally, an adaptive region weighting method is built for further strengthening the original nearest neighbor classifier in the feature matching stage. The extensive experiments carried out on an open texture database (Outex) and an actual surface defect database (Dragon) indicates that our proposed SDLBP yields promising performance on both classification accuracy and time efficiencyPeer reviewe

On NIS-Apriori Based Data Mining in SQL

We have proposed a framework of Rough Non-deterministic Information Analysis (RNIA) for tables with non-deterministic information, and applied RNIA to analyzing tables with uncertainty. We have also developed the RNIA software tool in Prolog and getRNIA in Python, in addition to these two tools we newly consider the RNIA software tool in SQL for handling large size data sets. This paper reports the current state of the prototype named NIS-Apriori in SQL, which will afford us more convenient environment for data analysis.International Joint Conference on Rough Sets　(IJCRS 2016), October 7-11, 2016, Santiago, Chil

Design of gate-tunable graphene electro-optical reflectors based on an optical slot-antenna coupled cavity

The unique properties of graphene offer an exciting opportunity towards tunable photonic surfaces for flexible devices. In this paper, we design a gate-tunable, free-space graphene electro-optical reflector based on cavity resonator structures. We firstly calculate the graphene refractive index n and k as a function of Fermi level and external gating voltage. Then, we designed the structure of the single-layer graphene reflective resonator by carefully selecting suitable materials and device parameters to maximize the reflectance differences before and after electro-optical tuning. We also developed a theoretical model to discuss this system based on the optical transition matrix method. Moreover, we used field enhancement to further increase the reflectance differences by incorporating Sn nanodots based optical slot-antenna coupled cavities. The maximum broadband, incident angle insensitive reflectance differences could reach 28% with an extinction ratio of 1.62 dB at a low insertion loss of 0.45 dB, and the spectral range is tunable by changing the optical cavity length. We also used an indium tin oxide layer as part of the optical cavity and the electrode simultaneously to reduce the voltage applied. To our best knowledge, this work is the first one on tunable two-dimensional (2D) material reflectors for free-space applications, apart from using liquid crystals or magnetic metasurfaces. This new design of tunable 2D electro-optical reflectors also reduces the complexity of fabrication steps, having promising applications in tunable flexible photonic surfaces and devices for variable optical attenuators and light detection and ranging systems