De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing

published_or_final_versio

Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars

BACKGROUND: In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) and trans-acting siRNAs (tasiRNAs) biogenesis were significantly changed in the fast-growing lines. In this study, the sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed. RESULTS: 9-13 million reads from each library were mapped to genome. miRNAs, tasiRNAs and natural antisense transcripts-generated small interfering RNAs (natsiRNAs) were identified and compared between libraries. In the leaf of OE lines, 15 known miRNAs increased in abundance and 9 miRNAs decreased in abundance, whereas in the root of OE lines, 2 known miRNAs increased in abundance and 9 miRNAs decreased in abundance. miRNAs with increased abundance in the leaf and root samples of both OE lines (miR158b and miR172a/b) were predicted to target mRNAs coding for Dof zinc finger protein and Apetala 2 (AP2) proteins, respectively. Furthermore, a significant change in the miR173-tasiRNAs-PPR/TPR network was observed in the leaves of both OE lines. CONCLUSION: In this study, the impact of high energy content on the sRNA profiles of Arabidopsis is reported. While the abundance of many stress-induced miRNAs is unaltered, the abundance of some miRNAs related to plant growth and development (miR172 and miR319) is elevated in the fast-growing lines. An induction of miR173-tasiRNAs-PPR/TPR network was also observed in the OE lines. In contrast, only few cis- and trans-natsiRNAs are altered in the fast-growing lines.published_or_final_versio

Demystifying construction project time-effort distribution curves: a BIM and non-BIM comparison

MacLeamy's time-effort distribution curves are among the most oft-cited sources for researchers interested in mainstreaming building information modeling (BIM) implementation in the architecture, engineering, and construction (AEC) industry. Succinctly, the curves offer a clever answer to the question: How can BIM benefit AEC processes? However, despite their significant theoretical and practical value, little previous research has been conducted to elaborate the time-effort distribution curves of any real-life projects. This research aims to demystify the time-effort distribution curves through comparison of a representative BIM project and a non-BIM project. Applying a set of innovative approaches, the actual time-effort distribution curves of two public housing construction projects in Hong Kong are produced and analyzed in-depth. The curves vividly show that BIM implementation increases the effort spent at design stage - that is, throughout the architecture and engineering processes - but the extra effort pays off at the building stage. Further, the curves are found to be a useful graphical analytic tool for other purposes, such as adjusting the fee structure among AEC processes and informing improved BIM adoption.postprin

Towards a better similarity measure for keyword profiling via clustering

Automatic profiling for users and postings can help law enforcement units cluster and classify users and postings effectively so that potential problematic users and postings can be identified easily. A core problem in this application is to come up with effective profiles and a good measure to compare the similarity of two profiles. In this paper, we investigate an existing keyword-based user profiling scheme and identify its limitations. Then, we propose an improved version of it and demonstrate that our proposed version is more consistent than the existing approach with respect to the observed replied rates of a user to a posting based on the similarity of the profiles. © 2013 IEEE.published_or_final_versio

A comparison of acidic and enzymatic hydrolysis of rutin

Rutin and its hydrolysis products (isoquercitrin and quercetin) are widely used as important materials in food and pharmaceutical industry. In this study, the effects of various acids and enzymes as catalysts on the hydrolysis reaction of rutin were studied. In comparison with acidic and enzymatic catalysis of rutin, the research results indicated that there was a sharp difference in the selectivity of hydrolysis product between the methods. When 2.5% H3PO4, 1% HCl and 0.5% H2SO4 were used as catalysts, transformation yields of isoquercitin hydrolyzed from rutin were 9.60, 0.69 and 1.25%, but those of quercetin were 11.13, 100 and 2.57%, respectively. When hesperidinase, snailase and cellulase-T2440 were used as catalysts, transformation yields of isoquercitin hydrolyzed from rutin were 43.21, 3.07 and 0.00%, but those of quercetin were 58.10, 96.39 and 30.89%, respectively. In conclusion, the aglycon of rutin was deglycosolated easily under mild acidic hydrolysis conditions at appropriate temperatures, but its secondary glucoside was difficult to be obtained. Contrarily, the prepared isoquercitrin by enzymatic hydrolysis of rutin was preferable to the acidic hydrolysis, especially for hesperidinase.Key words: Rutin, isoquercitrin, quercetin, hydrolysis, acid, enzym

Nonequilibrium Singlet-Triplet Kondo Effect in Carbon Nanotubes

The Kondo-effect is a many-body phenomenon arising due to conduction electrons scattering off a localized spin. Coherent spin-flip scattering off such a quantum impurity correlates the conduction electrons and at low temperature this leads to a zero-bias conductance anomaly. This has become a common signature in bias-spectroscopy of single-electron transistors, observed in GaAs quantum dots as well as in various single-molecule transistors. While the zero-bias Kondo effect is well established it remains uncertain to what extent Kondo correlations persist in non-equilibrium situations where inelastic processes induce decoherence. Here we report on a pronounced conductance peak observed at finite bias-voltage in a carbon nanotube quantum dot in the spin singlet ground state. We explain this finite-bias conductance anomaly by a nonequilibrium Kondo-effect involving excitations into a spin triplet state. Excellent agreement between calculated and measured nonlinear conductance is obtained, thus strongly supporting the correlated nature of this nonequilibrium resonance.Comment: 21 pages, 5 figure

Estimating equations for biomarker based exposure estimation under non-steady-state conditions

Unrealistic steady-state assumptions are often used to estimate toxicant exposure rates from biomarkers. A biomarker may instead be modeled as a weighted sum of historical time-varying exposures. Estimating equations are derived for a zero-inflated gamma distribution for daily exposures with a known exposure frequency. Simulation studies suggest that the estimating equations can provide accurate estimates of exposure magnitude at any reasonable sample size, and reasonable estimates of the exposure variance at larger sample sizes

Orbital Kondo effect in carbon nanotubes

Progress in the fabrication of nanometer-scale electronic devices is opening new opportunities to uncover the deepest aspects of the Kondo effect, one of the paradigmatic phenomena in the physics of strongly correlated electrons. Artificial single-impurity Kondo systems have been realized in various nanostructures, including semiconductor quantum dots, carbon nanotubes and individual molecules. The Kondo effect is usually regarded as a spin-related phenomenon, namely the coherent exchange of the spin between a localized state and a Fermi sea of electrons. In principle, however, the role of the spin could be replaced by other degrees of freedom, such as an orbital quantum number. Here we demonstrate that the unique electronic structure of carbon nanotubes enables the observation of a purely orbital Kondo effect. We use a magnetic field to tune spin-polarized states into orbital degeneracy and conclude that the orbital quantum number is conserved during tunneling. When orbital and spin degeneracies are simultaneously present, we observe a strongly enhanced Kondo effect, with a multiple splitting of the Kondo resonance at finite field and predicted to obey a so-called SU(4) symmetry.Comment: 26 pages, including 4+2 figure