Integrated management of Fusarium wilt of bananas in the Philippines and Australia

This project aimed to improve the long-term management of Fusarium wilt and the livelihoods of smallholders and communities dependent on export Cavendish bananas production. Fusarium wilt is the biggest threat to the Philippines’ substantial Cavendish bananas export industry, impacting the trade and livelihoods of smallholder banana producers. About 10% of the land currently used for export production in Mindanao is infected with Fusarium wilt, which is continuing to spread, with differing degrees of severity. The export industry could be wiped out in as little as five years if Fusarium wilt of bananas is not controlled in Mindanao. This would disrupt the livelihoods of up to 300,000 families. This project aimed to develop techniques to limit Fusarium wilt losses to smallholder Cavendish production in Davao del Norte and Ladyfinger production in Australia; evaluate the effectiveness of integrated crop management approaches in enabling commercial banana production where Fusarium wilt is present; and determine barriers to adoption of systems to suppress Fusarium wilt in banana production

First results from the Very Small Array -- I. Observational methods

The Very Small Array (VSA) is a synthesis telescope designed to image faint structures in the cosmic microwave background on degree and sub-degree angular scales. The VSA has key differences from other CMB interferometers with the result that different systematic errors are expected. We have tested the operation of the VSA with a variety of blank-field and calibrator observations and cross-checked its calibration scale against independent measurements. We find that systematic effects can be suppressed below the thermal noise level in long observations; the overall calibration accuracy of the flux density scale is 3.5 percent and is limited by the external absolute calibration scale.Comment: 9 pages, 10 figures, MNRAS in press (Minor revisions

Elevated urinary CRELD2 is associated with endoplasmic reticulum stress-mediated kidney disease

ER stress has emerged as a signaling platform underlying the pathogenesis of various kidney diseases. Thus, there is an urgent need to develop ER stress biomarkers in the incipient stages of ER stress-mediated kidney disease, when a kidney biopsy is not yet clinically indicated, for early therapeutic intervention. Cysteine-rich with EGF-like domains 2 (CRELD2) is a newly identified protein that is induced and secreted under ER stress. For the first time to our knowledge, we demonstrate that CRELD2 can serve as a sensitive urinary biomarker for detecting ER stress in podocytes or renal tubular cells in murine models of podocyte ER stress-induced nephrotic syndrome and tunicamycin- or ischemia-reperfusion-induced acute kidney injury (AKI), respectively. Most importantly, urinary CRELD2 elevation occurs in patients with autosomal dominant tubulointerstitial kidney disease caused by UMOD mutations, a prototypical tubular ER stress disease. In addition, in pediatric patients undergoing cardiac surgery, detectable urine levels of CRELD2 within postoperative 6 hours strongly associate with severe AKI after surgery. In conclusion, our study has identified CRELD2 as a potentially novel urinary ER stress biomarker with potential utility in early diagnosis, risk stratification, treatment response monitoring, and directing of ER-targeted therapies in selected patient subgroups in the emerging era of precision nephrology

Estimating the bispectrum of the Very Small Array data

We estimate the bispectrum of the Very Small Array data from the compact and extended configuration observations released in December 2002, and compare our results to those obtained from Gaussian simulations. There is a slight excess of large bispectrum values for two individual fields, but this does not appear when the fields are combined. Given our expected level of residual point sources, we do not expect these to be the source of the discrepancy. Using the compact configuration data, we put an upper limit of 5400 on the value of f_NL, the non-linear coupling parameter, at 95 per cent confidence. We test our bispectrum estimator using non-Gaussian simulations with a known bispectrum, and recover the input values.Comment: 17 pages, 16 figures, replaced with version accepted by MNRAS. Primordial bispectrum recalculated and figure 11 change

Modified qHAADF method for atomic column-by-column compositional quantification of semiconductor heterostructures

The qHAADF method allows the quantification of the composition at atomic column resolution in semiconductor materials by comparing the HAADF-STEM intensities between a region of interest to a region of the material of known composition. However, the application of this qHAADF approach requires both regions to be differentiable and included in the same micrograph at close proximity. This limits the application of this approach to certain materials and magnifications where this requirement is fulfilled. In this work, we extend the qHAADF method to analyses where the reference region is imaged in a separate micrograph. The validity of this modified method is proved by comparison to the original qHAADF approach using HAADF-STEM simulated images of the semiconductor heterostructure InSb/InAs. Additionally, the methods are applied successfully to experimental images both of a simple InSb/InAs interface and of a complex InSb/GaSb heterostructure, justifying the significance of the modified method over the original method

Effect of the cap layer growth temperature on the Sb distribution in InAs/InSb/InAs sub-monolayer heterostructures for mid-infrared devices

Sub-monolayer (SML) deposition of InSb within InAs matrix by migration enhanced epitaxy (MEE) tends to form type II SML nanostructures offering efficient light emission within the mid-infrared (MIR) range between 3-5 µm. In this work, we report on the Sb distribution in InSb/InAs SML nanostructures with InAs cap layers grown at temperatures lower than that associated with the under-grown InSb active layer. Analysis by transmission electron microscopy (TEM) in 002 dark field (DF) conditions shows that the reduction in the growth temperature of the InAs cap layer increases the amount of Sb deposited in the layers, in good agreement with the X-ray diffraction (XRD) results. TEM micrographs also show that the layers are formed by random InSbAs agglomerates, where the lower cap temperature leads to a more continuous InSb layer. Quantitative atomic column resolved high angle annular dark field (HAADF)-scanning (S)TEM analyses also reveal atomic columns with larger composition of Sb for the structure with the lowest InAs cap layer temperature. The dependence of the Sb distribution on InAs cap growth temperature allows tuning the corresponding emission wavelength in the MIR range, as shown by the photoluminescence (PL) emission spectra

Searching for non-Gaussianity in the VSA data

We have tested Very Small Array (VSA) observations of three regions of sky for the presence of non-Gaussianity, using high-order cumulants, Minkowski functionals, a wavelet-based test and a Bayesian joint power spectrum/non-Gaussianity analysis. We find the data from two regions to be consistent with Gaussianity. In the third region, we obtain a 96.7% detection of non-Gaussianity using the wavelet test. We perform simulations to characterise the tests, and conclude that this is consistent with expected residual point source contamination. There is therefore no evidence that this detection is of cosmological origin. Our simulations show that the tests would be sensitive to any residual point sources above the data's source subtraction level of 20 mJy. The tests are also sensitive to cosmic string networks at an rms fluctuation level of $105 \mu K$ (i.e. equivalent to the best-fit observed value). They are not sensitive to string-induced fluctuations if an equal rms of Gaussian CDM fluctuations is added, thereby reducing the fluctuations due to the strings network to $74 \mu K$ rms . We especially highlight the usefulness of non-Gaussianity testing in eliminating systematic effects from our data.Comment: Minor corrections; accepted for publication to MNRA

Cosmological parameter estimation using Very Small Array data out to l=1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other CMB data and external priors. Within the flat $\Lambda$CDM model, we find that the inclusion of high resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by WMAP alone, while still remaining compatible with their estimates. We find that $\Omega_{\rm b}h^2=0.0234^{+0.0012}_{-0.0014}$, $\Omega_{\rm dm}h^2=0.111^{+0.014}_{-0.016}$, $h=0.73^{+0.09}_{-0.05}$, $n_{\rm S}=0.97^{+0.06}_{-0.03}$, $10^{10}A_{\rm S}=23^{+7}_{-3}$ and $\tau=0.14^{+0.14}_{-0.07}$ for WMAP and VSA when no external prior is included.On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95% confidence ($n_{\rm run}=-0.069\pm 0.032$), something which is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of $\Omega_{\rm m}$. We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that $f_{\nu}< 0.087$ at 95% confidence which corresponds to $m_\nu<0.32{\rm eV}$ when all neutrino masses are the equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for $n_{\rm run}<0$ is only marginal within this model