Rapid identification of allergenic and pathogenic molds in environmental air by an oligonucleotide array

<p>Abstract</p> <p>Background</p> <p>Airborne fungi play an important role in causing allergy and infections in susceptible people. Identification of these fungi, based on morphological characteristics, is time-consuming, expertise-demanding, and could be inaccurate.</p> <p>Methods</p> <p>We developed an oligonucleotide array that could accurately identify 21 important airborne fungi (13 genera) that may cause adverse health problems. The method consisted of PCR amplification of the internal transcribed spacer (ITS) regions, hybridization of the PCR products to a panel of oligonucleotide probes immobilized on a nylon membrane, and detection of the hybridization signals with alkaline phosphatase-conjugated antibodies.</p> <p>Results</p> <p>A collection of 72 target and 66 nontarget reference strains were analyzed by the array. Both the sensitivity and specificity of the array were 100%, and the detection limit was 10 pg of genomic DNA per assay. Furthermore, 70 fungal isolates recovered from air samples were identified by the array and the identification results were confirmed by sequencing of the ITS and D1/D2 domain of the large-subunit RNA gene. The sensitivity and specificity of the array for identification of the air isolates was 100% (26/26) and 97.7% (43/44), respectively.</p> <p>Conclusions</p> <p>Identification of airborne fungi by the array was cheap and accurate. The current array may contribute to decipher the relationship between airborne fungi and adverse health effect.</p

An efficient surrogate model for emulation and physics extraction of large eddy simulations

In the quest for advanced propulsion and power-generation systems, high-fidelity simulations are too computationally expensive to survey the desired design space, and a new design methodology is needed that combines engineering physics, computer simulations and statistical modeling. In this paper, we propose a new surrogate model that provides efficient prediction and uncertainty quantification of turbulent flows in swirl injectors with varying geometries, devices commonly used in many engineering applications. The novelty of the proposed method lies in the incorporation of known physical properties of the fluid flow as {simplifying assumptions} for the statistical model. In view of the massive simulation data at hand, which is on the order of hundreds of gigabytes, these assumptions allow for accurate flow predictions in around an hour of computation time. To contrast, existing flow emulators which forgo such simplications may require more computation time for training and prediction than is needed for conducting the simulation itself. Moreover, by accounting for coupling mechanisms between flow variables, the proposed model can jointly reduce prediction uncertainty and extract useful flow physics, which can then be used to guide further investigations.Comment: Submitted to JASA A&C

Applicability of perturbative QCD to Λb→Λc\Lambda_b \to \Lambda_c decays

We develop perturbative QCD factorization theorem for the semileptonic heavy baryon decay $\Lambda_b \to \Lambda_c l\bar{\nu}$, whose form factors are expressed as the convolutions of hard $b$ quark decay amplitudes with universal $\Lambda_b$ and $\Lambda_c$ baryon wave functions. Large logarithmic corrections are organized to all orders by the Sudakov resummation, which renders perturbative expansions more reliable. It is observed that perturbative QCD is applicable to $\Lambda_b \to \Lambda_c$ decays for velocity transfer greater than 1.2. Under requirement of heavy quark symmetry, we predict the branching ratio $B(\Lambda_b \to \Lambda_c l{\bar\nu})\sim 2$, and determine the $\Lambda_b$ and $\Lambda_c$ baryon wave functions.Comment: 12 pages in Latex file, 3 figures in postscript files, some results are changed, but the conclusion is the sam

The effect of typhoon on particulate organic carbon flux in the southern East China Sea

Severe tropical storms play an important role in triggering phytoplankton blooms, but the extent to which such storms influence biogenic carbon flux from the euphotic zone is unclear. In 2008, typhoon Fengwong provided a unique opportunity to study the in situ biological responses including phytoplankton blooms and particulate organic carbon fluxes associated with a severe storm in the southern East China Sea (SECS). After passage of the typhoon, the sea surface temperature (SST) in the SECS was markedly cooler (&amp;sim;25 to 26 °C) than before typhoon passage (&amp;sim;28 to 29 °C). The POC flux 5 days after passage of the typhoon was 265 &amp;plusmn; 14 mg C m&lt;sup&gt;−2&lt;/sup&gt; d&lt;sup&gt;−1&lt;/sup&gt;, which was &amp;sim;1.7-fold that (140–180 mg C m&lt;sup&gt;−2&lt;/sup&gt; d&lt;sup&gt;−1&lt;/sup&gt;) recorded during a period (June–August, 2007) when no typhoons occurred. A somewhat smaller but nevertheless significant increase in POC flux (224–225 mg C m&lt;sup&gt;−2&lt;/sup&gt; d&lt;sup&gt;−1&lt;/sup&gt;) was detected following typhoon Sinlaku which occurred approximately 1 month after typhoon Fengwong, indicating that typhoon events can increase biogenic carbon flux efficiency in the SECS. Remarkably, phytoplankton uptake accounted for only about 5% of the nitrate injected into the euphotic zone by typhoon Fengwong. It is likely that phytoplankton population growth was constrained by a combination of light limitation and grazing pressure. Modeled estimates of new/export production were remarkably consistent with the average of new and export production following typhoon Fengwong. The same model suggested that during non-typhoon conditions approximately half of the export of organic carbon occurs via convective mixing of dissolved organic carbon, a conclusion consistent with earlier work at comparable latitudes in the open ocean

Intra- and Inter-Individual Variance of Gene Expression in Clinical Studies

BACKGROUND: Variance in microarray studies has been widely discussed as a critical topic on the identification of differentially expressed genes; however, few studies have addressed the influence of estimating variance. METHODOLOGY/PRINCIPAL FINDINGS: To break intra- and inter-individual variance in clinical studies down to three levels--technical, anatomic, and individual--we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of "inter-individual variable genes" were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduces/eliminates the effects of underestimated variance. CONCLUSIONS/SIGNIFICANCE: Our data demonstrated that correct variance evaluation is critical in selecting significant genes. If the degree of variance is underestimated, "noisy" genes are falsely identified as differentially expressed genes. These genes are the noise associated with biological interpretation, reducing the biological significance of the gene set. Our results also indicate that applying a higher number of fold change as the selection criteria reduces/eliminates the differences between distinct estimations of variance

Perturbative QCD analysis of B→ϕK∗B \to \phi K^* decays

We study the first observed charmless $B\to VV$ modes, the $B\to\phi K^*$ decays, in perturbative QCD formalism. The obtained branching ratios $B(B\to\phi K^*)\sim 15 \times 10^{-6}$ are larger than $\sim 9\times 10^{-6}$ from QCD factorization. The comparison of the predicted magnitudes and phases of the different helicity amplitudes, and branching ratios with experimental data can test the power counting rules, the evaluation of annihilation contributions, and the mechanism of dynamical penguin enhancement in perturbative QCD, respectively.Comment: 14 pages, 2 tables, brief disscussion on hard sacle added, version to appear in PR

Final state interaction and B→KKB\to KK decays in perturbative QCD

We predict branching ratios and CP asymmetries of the $B\to KK$ decays using perturbative QCD factorization theorem, in which tree, penguin, and annihilation contributions, including both factorizable and nonfactorizable ones, are expressed as convolutions of hard six-quark amplitudes with universal meson wave functions. The unitarity angle $\phi_3= 90^o$ and the $B$ and $K$ meson wave functions extracted from experimental data of the $B\to K\pi$ and $\pi\pi$ decays are employed. Since the $B\to KK$ decays are sensitive to final-state-interaction effects, the comparision of our predictions with future data can test the neglect of these effects in the above formalism. The CP asymmetry in the $B^\pm\to K^\pm K^0$ modes and the $B_d^0\to K^\pm K^\mp$ branching ratios depend on annihilation and nonfactorizable amplitudes. The $B\to KK$ data can also verify the evaluation of these contributions.Comment: 13 pages in latex file, 7 figures in ps file

Deep ultraviolet laser direct write for patterning sol-gel InGaZnO semiconducting micro/nanowires and improving field-effect mobility

Deep-UV (DUV) laser was used to directly write indium-gallium-zinc-oxide (IGZO) precursor solution and form micro and nanoscale patterns. The directional DUV laser beam avoids the substrate heating and suppresses the diffraction effect. A IGZO precursor solution was also developed to fulfill the requirements for direct photopatterning and for achieving semi-conducting properties with thermal annealing at moderate temperature. The DUV-induced crosslinking of the starting material allows direct write of semi-conducting channels in thin-film transistors but also it improves the field-effect mobility and surface roughness. Material analysis has been carried out by XPS, FTIR, spectroscopic ellipsometry and AFM and the effect of DUV on the final material structure is discussed. The DUV irradiation step results in photolysis and a partial condensation of the inorganic network that freezes the sol-gel layer in a homogeneous distribution, lowering possibilities of thermally induced reorganization at the atomic scale. Laser irradiation allows high-resolution photopatterning and high-enough field-effect mobility, which enables the easy fabrication of oxide nanowires for applications in solar cell, display, flexible electronics, and biomedical sensors