WEB-GIS BASED BRIDGE INFORMATION DATABASE VISUALIZATION ANALYTICS AND DISTRIBUTED SENSING FRAMEWORK

The national bridge system plays very important role in society operations ensuring mobilities that can sustain social and economic growth. Recent increasingly growing concerns about the safety of existing bridges are shared by highway agencies at all levels of government, including federal, state and municipal. To provide a user-friendly and effective environment and services for accessing and analyzing the National Bridge Inventory (NBI) database, a powerful bridge data management system needs be developed to assist the bridge managers or professionals to manage and maintain effectively and efficiently the national bridge system. The objective of this research is to develop a Web-GIS (geographic information system) based bridge information database visualization analytics and distributed sensing framework for nation-wide bridge system management. This is accomplished by integrating modern technologies including GIS, Internet, database, remote sensing, visualization, and smartphone technologies. The objectives of this study include: 1) establishment of a system framework for effective use of current available bridge condition data and volunteering sensing data; 2) development of visualization and visual analytic applications appropriate for bridge information; 3) development of user-defined criteria query for decision-making support; and 4) development of a remote sensing database to aid engineers and other professionals in accessing, retrieving and manipulating information from the bridge database. The citizen-based sensors for bridge monitoring utilize voluntary information-sharing from individuals as a monitoring technique. The Web-GIS based Bridge Management System (BMS) framework developed in this research allows centralized data collection and data visualization analytics at any place and any time. It is intended as a critical step towards rapid bridge diagnostics using an integrated sensing data approach. Current bridge management is predominantly at state level. Furthermore, by adopting the “citizen sensor” concept, public data can be added into the bridge database as additional information for bridge management. The outcome of this research is a framework called: “Bridge-WGI.” The six critical modules formed the core of the framework, which are: 1) bridge database systems; 2) general bridge information visualization; 3) bridge information analytical visualization; 4) user-defined criteria query; 5) citizen sensing application in bridge monitoring; and 6) remote sensing database application. The Bridge-WGI framework demonstrates the capabilities of Web-based BMS can be accomplished via the integration of several technologies. These capabilities include: 1) application of volunteering sensing; 2) flexible accessibility via Internet; 3) several advanced visualization of bridge data; 4) bridge data integration; and 5) online user- defined query for decision making support

Geometric phase outside a Schwarzschild black hole and the Hawking effect

We study the Hawking effect in terms of the geometric phase acquired by a two-level atom as a result of coupling to vacuum fluctuations outside a Schwarzschild black hole in a gedanken experiment. We treat the atom in interaction with a bath of fluctuating quantized massless scalar fields as an open quantum system, whose dynamics is governed by a master equation obtained by tracing over the field degrees of freedom. The nonunitary effects of this system are examined by analyzing the geometric phase for the Boulware, Unruh and Hartle-Hawking vacua respectively. We find, for all the three cases, that the geometric phase of the atom turns out to be affected by the space-time curvature which backscatters the vacuum field modes. In both the Unruh and Hartle-Hawking vacua, the geometric phase exhibits similar behaviors as if there were thermal radiation at the Hawking temperature from the black hole. So, a measurement of the change of the geometric phase as opposed to that in a flat space-time can in principle reveal the existence of the Hawking radiation.Comment: 14 pages, no figures, a typo in the References corrected, version to appear in JHEP. arXiv admin note: text overlap with arXiv:1109.033

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Single-Peptide TR-FRET Detection Platform for Cysteine-Specific Post-Translational Modifications

Post-translational modifications (PTMs) are one of the most important regulatory mechanisms in cells, and they play key roles in cell signaling both in health and disease. PTM catalyzing enzymes have become significant drug targets, and therefore, tremendous interest has been focused on the development of broad-scale assays to monitor several different PTMs with a single detection platform. Most of the current methodologies suffer from low throughput or rely on antibody recognition, increasing the assay costs, and decreasing the multifunctionality of the assay. Thus, we have developed a sensitive time-resolved Forster resonance energy transfer (TR-FRET) detection method for PTMs of cysteine residues using a single-peptide approach performed in a 384-well format. In the developed assay, the enzyme-specific biotinylated substrate peptide is post-translationally modified at the cysteine residue, preventing the subsequent thiol coupling with a reactive AlexaFluor 680 acceptor dye. In the absence of enzymatic activity, increase in the TR-FRET signal between the biotin-bound Eu(III)-labeled streptavidin donor and the cysteine-coupled AlexaFluor 680 acceptor dye is observed. We demonstrate the detection concept with cysteine modifying S-nitrosylation and ADP-ribosylation reactions using a chemical nitric oxide donor S-nitrosoglutathione and enzymatic ADP-ribosyltransferase PtxS1-subunit of pertussis toxin, respectively. As a proof of concept, three peptide substrates derived from the small GTPase K-Ras and the inhibitory alpha-subunit of the heterotrimeric G-protein G alpha i showed expected functionality in both chemical and enzymatic assays. Measurements yielded signal-to-background ratios of 28.7, 33.0, and 8.7 between the modified and the nonmodified substrates for the three peptides in the S-nitrosylation assay, 5.8 in the NAD(+) hydrolysis assay, and 6.8 in the enzymatic ADP-ribosyltransferase inhibitor dose-response assay. The developed antibody-free assay for cysteine-modifying enzymes provides a detection platform with low nanomolar peptide substrate consumption, and the assay is potentially applicable to investigate various cysteine-modifying enzymes in a high throughput compatible format

Impact of Insecticides on Parasitoids of the Leafminer, Liriomyza trifolii, in Pepper in South Texas

Liriomyza leafminers (Diptera: Agromyzidae) are cosmopolitan, polyphagous pests of horticultural plants and many are resistant to insecticides. Producers in South Texas rely on insecticides as the primary management tool for leafminers, and several compounds are available. The objective of this study is to address the efficacy of these compounds for controlling Liriomyza while minimizing their effects against natural enemies. Research plots were established at Texas AgriLife research center at Weslaco, Texas in fall 2007 and spring 2008 seasons, and peppers were used as a model crop. Plots were sprayed with novaluron, abamectin, spinetoram, lambda-cyhalothrin and water as treatments according to leafminer infestation; insecticide efficacy was monitored by collecting leaves and infested foliage. Plant phenology was also monitored. Novaluron was the most effective insecticide and lambda-cyhalothrin showed resurgence in leafminer density in fall 2007 and no reduction in spring 2008. Other compounds varied in efficacy. Novaluron showed the least number of parasitoids per leafminer larva and the lowest parasitoid diversity index among treatments followed by spinetoram. Liriomyza trifolii (Burgess) was the sole leafminer species on peppers, and 19 parasitoid species were found associated with this leafminer. Application of these insecticides for management of leafminers with conservation of natural enemies is discussed

Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of ascaris reveals a novel fold and two discrete lipid-binding sites

Parasitic nematode worms cause serious health problems in humans and other animals. They can induce allergic-type immune responses, which can be harmful but may at the same time protect against the infections. Allergens are proteins that trigger allergic reactions and these parasites produce a type that is confined to nematodes, the nematode polyprotein allergens (NPAs). These are synthesized as large precursor proteins comprising repeating units of similar amino acid sequence that are subsequently cleaved into multiple copies of the allergen protein. NPAs bind small lipids such as fatty acids and retinol (Vitamin A) and probably transport these sensitive and insoluble compounds between the tissues of the worms. Nematodes cannot synthesize these lipids, so NPAs may also be crucial for extracting nutrients from their hosts. They may also be involved in altering immune responses by controlling the lipids by which the immune and inflammatory cells communicate. We describe the molecular structure of one unit of an NPA, the well-known ABA-1 allergen of Ascaris and find its structure to be of a type not previously found for lipid-binding proteins, and we describe the unusual sites where lipids bind within this structur

Suspension culture combined with chemotherapeutic agents for sorting of breast cancer stem cells

<p>Abstract</p> <p>Background</p> <p>Cancer stem cell (CSC) hypothesis has not been well demonstrated by the lack of the most convincing evidence concerning a single cell capable of giving rise to a tumor. The scarcity in quantity and improper approaches for isolation and purification of CSCs have become the major obstacles for great development in CSCs. Here we adopted suspension culture combined with anticancer regimens as a strategy for screening breast cancer stem cells (BrCSCs). BrCSCs could survive and be highly enriched in non-adherent suspension culture while chemotherapeutic agents could destroy most rapidly dividing cancer cells and spare relatively quiescent BrCSCs.</p> <p>Methods</p> <p>TM40D murine breast cancer cells were cultured in serum-free medium. The expression of CD44⁺CD24^-was measured by flow cytometry. Cells of passage 10 were treated in combination with anticancer agents pacilitaxel and epirubicin at different peak plasma concentrations for 24 hours, and then maintained under suspension culture. The rate of apoptosis was examined by flow cytometry with Annexin-V fluorescein isothiocyanate (FITC)/propidium iodide (PI) double staining method. Selected cells in different amounts were injected subcutaneously into BALB/C mice to observe tumor formation.</p> <p>Results</p> <p>Cells of passage 10 in suspension culture had the highest percentage of CD44⁺CD24^-(about 77 percent). A single tumor cell in 0.35 PPC could generate tumors in 3 of 20 BALB/C mice.</p> <p>Conclusion</p> <p>Suspension culture combined with anticancer regimens provides an effective means of isolating, culturing and purifying BrCSCs.</p

A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues

Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure composition of the active site and its similarity to known active sites containing redox Cys and (ii) calculating accessibility, active site location, and reactivity of Cys. For proteins with known or modeled structures, this method can identify proteins with catalytic Cys residues and distinguish thiol oxidoreductases from the enzymes containing other catalytic Cys types. Furthermore, by applying this procedure to Saccharomyces cerevisiae proteins containing conserved Cys, we could identify the majority of known yeast thiol oxidoreductases. This study provides insights into the structural properties of catalytic redox-active Cys and should further help to recognize thiol oxidoreductases in protein sequence and structure databases

Transcriptome Profiling of Human Pre-Implantation Development

BACKGROUND: Preimplantation development is a crucial step in early human development. However, the molecular basis of human preimplantation development is not well known. METHODOLOGY: By applying microarray on 397 human oocytes and embryos at six developmental stages, we studied the transcription dynamics during human preimplantation development. PRINCIPAL FINDINGS: We found that the preimplantation development consisted of two main transitions: from metaphase-II oocyte to 4-cell embryo where mainly the maternal genes were expressed, and from 8-cell embryo to blastocyst with down-regulation of the maternal genes and up-regulation of embryonic genes. Human preimplantation development proved relatively autonomous. Genes predominantly expressed in oocytes and embryos are well conserved during evolution. SIGNIFICANCE: Our database and findings provide fundamental resources for understandin