Infrastructure Engineering - Research Publications
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ItemMachine learning-derived gut microbiome signature predicts fatty liver disease in the presence of insulin resistance(NATURE PORTFOLIO, 2022-12-17)A simple predictive biomarker for fatty liver disease is required for individuals with insulin resistance. Here, we developed a supervised machine learning-based classifier for fatty liver disease using fecal 16S rDNA sequencing data. Based on the Kangbuk Samsung Hospital cohort (n = 777), we generated a random forest classifier to predict fatty liver diseases in individuals with or without insulin resistance (n = 166 and n = 611, respectively). The model performance was evaluated based on metrics, including accuracy, area under receiver operating curve (AUROC), kappa, and F1-score. The developed classifier for fatty liver diseases performed better in individuals with insulin resistance (AUROC = 0.77). We further optimized the classifiers using genetic algorithm. The improved classifier for insulin resistance, consisting of ten microbial genera, presented an advanced classification (AUROC = 0.93), whereas the improved classifier for insulin-sensitive individuals failed to distinguish participants with fatty liver diseases from the healthy. The classifier for individuals with insulin resistance was comparable or superior to previous methods predicting fatty liver diseases (accuracy = 0.83, kappa = 0.50, F1-score = 0.89), such as the fatty liver index. We identified the ten genera as a core set from the human gut microbiome, which could be a diagnostic biomarker of fatty liver diseases for insulin resistant individuals. Collectively, these findings indicate that the machine learning classifier for fatty liver diseases in the presence of insulin resistance is comparable or superior to commonly used methods.
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ItemPyruvate dehydrogenase kinase 4 promotes ubiquitin-proteasome system-dependent muscle atrophy(WILEY, 2022-12)BACKGROUND: Muscle atrophy, leading to muscular dysfunction and weakness, is an adverse outcome of sustained period of glucocorticoids usage. However, the molecular mechanism underlying this detrimental condition is currently unclear. Pyruvate dehydrogenase kinase 4 (PDK4), a central regulator of cellular energy metabolism, is highly expressed in skeletal muscle and has been implicated in the pathogenesis of several diseases. The current study was designed to investigated and delineate the role of PDK4 in the context of muscle atrophy, which could be identified as a potential therapeutic avenue to protect against dexamethasone-induced muscle wasting. METHODS: The dexamethasone-induced muscle atrophy in C2C12 myotubes was evaluated at the molecular level by expression of key genes and proteins involved in myogenesis, using immunoblotting and qPCR analyses. Muscle dysfunction was studied in vivo in wild-type and PDK4 knockout mice treated with dexamethasone (25 mg/kg body weight, i.p., 10 days). Body weight, grip strength, muscle weight and muscle histology were assessed. The expression of myogenesis markers were analysed using qPCR, immunoblotting and immunoprecipitation. The study was extended to in vitro human skeletal muscle atrophy analysis. RESULTS: Knockdown of PDK4 was found to prevent glucocorticoid-induced muscle atrophy and dysfunction in C2C12 myotubes, which was indicated by induction of myogenin (0.3271 ± 0.102 vs 2.163 ± 0.192, ****P < 0.0001) and myosin heavy chain (0.3901 ± 0.047 vs. 0.7222 ± 0.082, **P < 0.01) protein levels and reduction of muscle atrophy F-box (10.77 ± 2.674 vs. 1.518 ± 0.172, **P < 0.01) expression. In dexamethasone-induced muscle atrophy model, mice with genetic ablation of PDK4 revealed increased muscle strength (162.1 ± 22.75 vs. 200.1 ± 37.09 g, ***P < 0.001) and muscle fibres (54.20 ± 11.85% vs. 84.07 ± 28.41%, ****P < 0.0001). To explore the mechanism, we performed coimmunoprecipitation and liquid chromatography-mass spectrometry analysis and found that myogenin is novel substrate of PDK4. PDK4 phosphorylates myogenin at S43/T57 amino acid residues, which facilitates the recruitment of muscle atrophy F-box to myogenin and leads to its subsequent ubiquitination and degradation. Finally, overexpression of non-phosphorylatable myogenin mutant using intramuscular injection prevented dexamethasone-induced muscle atrophy and preserved muscle fibres. CONCLUSIONS: We have demonstrated that PDK4 mediates dexamethasone-induced skeletal muscle atrophy. Mechanistically, PDK4 phosphorylates and degrades myogenin via recruitment of E3 ubiquitin ligase, muscle atrophy F-box. Rescue of muscle regeneration by genetic ablation of PDK4 or overexpression of non-phosphorylatable myogenin mutant indicates PDK4 as an amenable therapeutic target in muscle atrophy.
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ItemNo Preview AvailableImproved Trend-Aware Postprocessing of GCM Seasonal Precipitation Forecasts(AMER METEOROLOGICAL SOC, 2022-01)Abstract Climate trends have been observed over the recent decades in many parts of the world, but current global climate models (GCMs) for seasonal climate forecasting often fail to capture these trends. As a result, model forecasts may be biased above or below the trendline. In our previous research, we developed a trend-aware forecast postprocessing method to overcome this problem. The method was demonstrated to be effective for embedding observed trends into seasonal temperature forecasts. In this study, we further develop the method for postprocessing GCM seasonal precipitation forecasts. We introduce new formulation and evaluation features to cater for special characteristics of precipitation amounts, such as having a zero lower bound and highly positive skewness. We apply the improved method to calibrate ECMWF SEAS5 forecasts of seasonal precipitation for Australia. Our evaluation shows that the calibrated forecasts reproduce observed trends over the hindcast period of 36 years. In some regions where observed trends are statistically significant, forecast skill is greatly improved by embedding trends into the forecasts. In most regions, the calibrated forecasts outperform the raw forecasts in terms of bias, skill, and reliability. Wider applications of the new trend-aware postprocessing method are expected to boost user confidence in seasonal precipitation forecasts.
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ItemNo Preview AvailablePartitioning of Precipitation Into Terrestrial Water Balance Components Under a Drying Climate(AMER GEOPHYSICAL UNION, 2023-05)Abstract To accurately project future water availability under a drying climate, it is important to understand how precipitation is partitioned into other terrestrial water balance components, such as fluxes (evaporation, transpiration, runoff) and changes in storage (soil moisture, groundwater). Many studies have reported unexpected large runoff reductions during drought, particularly for multi‐year events, and some studies report a persistent change in partitioning even after the meteorological drought has ended. This study focused on understanding how actual evapotranspiration (AET) and change in subsurface storage (ΔS) respond to climate variability and change, examining Australia's Millennium Drought (MD, 1997–2009). The study initially conducted a catchment‐scale water balance analysis to investigate interactions between ΔS and AET. Then the water balance analysis was extended to regional scale to investigate ΔS using interpolated rainfall and discharge with remotely sensed AET. Lastly, we evaluated conceptual rainfall‐runoff model performance of two commonly used models against these water balance estimates. The evaluation of water‐balance‐derived ΔS against Gravity Recovery and Climate Experiment (GRACE) estimates shows a significant multiyear storage decline; however, with different rates. In contrast, AET rates (annualized) remained approximately constant before and during the MD, contrasting with some reports of evapotranspiration enhancement elsewhere. Overall, given AET remained approximately constant, drought‐induced precipitation reductions were partitioned into ΔS and streamflow. The employed conceptual rainfall‐runoff models failed to realistically represent AET during the MD, suggesting the need for improved conceptualization of processes. This study provides useful implications for explaining future hydrological changes if similar AET behavior is observed under a drying climate.
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ItemNo Preview AvailableTraining sample selection for robust multi-year within-season crop classification using machine learning(Elsevier BV, 2023-07-01)Within-season crop classification using multispectral imagery is an effective way to generate timely crop maps that can support water and crop management; however, developing such models is challenging due to limited satellite imagery and ground truth data available during the season. This study investigated ways to optimize the use of multi-year samples in a within-season crop classification model, aiming to enable accurate within-season crop mapping across years. Our study focused on classifying field-scale corn/maize, cotton, and rice in south-eastern Australia from 2013 to 2019. The crop classification model was based on the random forest and support vector machine algorithms applied to Landsat 8 multispectral bands. We designed four experiments to understand the influences of training sample selection on model accuracy. Specifically, we analyzed how the within-season classification accuracies are affected by 1) training sample size; 2) proportions of classification classes; 3) the inclusion of a non-crop class (e.g., fallow land) in the training sample, and 4) training samples collected from different years. We found that 1) the training sample size should be sufficiently large to ensure within-season classification accuracy; 2) using training samples for each crop type in proportion to their occurrence within the landscape results in more accurate multi-year classification; 3) the inclusion of the non-crop class can reduce the accuracy with which crop types are distinguished, so the proportion of the non-crop class should be maintained at a relatively low level, and 4) predicting the current year with training samples from previous years can lead to a minor decline in accuracy compared to using samples only from the current year. These training sample settings were adopted to develop a final model. We found that the model accuracy continues to improve as more input imagery is added as the cropping season progresses, with a rapid rate of initial improvement which then slows. December, the third month of the summer growing season, is the earliest time that reliable maps were generated, with an overall accuracy of 86 % and user's accuracies for all crops exceeding 80 %. Our proposed experiments are robust and transferable to other regions and seasons to assist the development of within-season crop maps, and can thus be valuable tools to support agricultural management.
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ItemExplaining changes in rainfall-runoff relationships during and after Australia's Millennium Drought: a community perspective(COPERNICUS GESELLSCHAFT MBH, 2022-12-06)Abstract. The Millennium Drought lasted more than a decade and is notable for causing persistent shifts in the relationship between rainfall and runoff in many southeastern Australian catchments. Research to date has successfully characterised where and when shifts occurred and explored relationships with potential drivers, but a convincing physical explanation for observed changes in catchment behaviour is still lacking. Originating from a large multi-disciplinary workshop, this paper presents and evaluates a range of hypothesised process explanations of flow response to the Millennium Drought. The hypotheses consider climatic forcing, vegetation, soil moisture dynamics, groundwater, and anthropogenic influence. The hypotheses are assessed against evidence both temporally (e.g. why was the Millennium Drought different to previous droughts?) and spatially (e.g. why did rainfall–runoff relationships shift in some catchments but not in others?). Thus, the strength of this work is a large-scale assessment of hydrologic changes and potential drivers. Of 24 hypotheses, 3 are considered plausible, 10 are considered inconsistent with evidence, and 11 are in a category in between, whereby they are plausible yet with reservations (e.g. applicable in some catchments but not others). The results point to the unprecedented length of the drought as the primary climatic driver, paired with interrelated groundwater processes, including declines in groundwater storage, altered recharge associated with vadose zone expansion, and reduced connection between subsurface and surface water processes. Other causes include increased evaporative demand and harvesting of runoff by small private dams. Finally, we discuss the need for long-term field monitoring, particularly targeting internal catchment processes and subsurface dynamics. We recommend continued investment in the understanding of hydrological shifts, particularly given their relevance to water planning under climate variability and change.
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ItemComparison of KOMPSAT-5 and Sentinel-1 Radar Data for Soil Moisture Estimations Using a New Semi-Empirical Model(MDPI, 2022-08)X-band KOMPSAT-5 provides a good perspective for soil moisture retrieval at high-spatial resolution over arid and semi-arid areas. In this paper, an intercomparison of KOMPSAT-5 and C-band Sentinel-1 radar data in soil moisture retrieval was conducted over agricultural fields in Wimmera, Victoria, Australia. Optical images from Sentinel-2 were also used to calculate the scattering contribution of vegetation. This study employed a new semi-empirical vegetation scattering model with a linear association of soil moisture with observed backscatter coefficient and vegetation indices. The Combined Vegetation Index (CVI) was proposed and first used to parameterize vegetation water content. As a result, the vegetation scattering model was developed to monitor soil moisture based on remotely sensed data and ground measurements. Application of the algorithm over dryland wheat field sites demonstrated that the estimated satellite-based soil moisture contents have good linear relationships with the ground measurements. The correlation coefficients (R) are 0.862 and 0.616, and the root mean square errors (RMSEs) have the values of 0.020 cm3/cm3 and 0.032 cm3/cm3 at X- and C-bands, respectively. Furthermore, the validation results also indicated that X-band provided higher consistent accuracy for soil moisture inversion than C-band. These results showed significant promise in retrieving soil moisture using KOMPSAT-5 and Sentinel-1 remotely sensed data at high-spatial resolution over agricultural fields, with subsequent uses for crop growth and yield estimation.
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ItemAn analysis framework to evaluate irrigation decisions using short-term ensemble weather forecasts(SPRINGER, 2023-01)Abstract Irrigation water is an expensive and limited resource and optimal scheduling can boost water efficiency. Scheduling decisions often need to be made several days prior to an irrigation event, so a key aspect of irrigation scheduling is the accurate prediction of crop water use and soil water status ahead of time. This prediction relies on several key inputs including initial soil water status, crop conditions and weather. Since each input is subject to uncertainty, it is important to understand how these uncertainties impact soil water prediction and subsequent irrigation scheduling decisions. This study aims to develop an uncertainty-based analysis framework for evaluating irrigation scheduling decisions under uncertainty, with a focus on the uncertainty arising from short-term rainfall forecasts. To achieve this, a biophysical process-based crop model, APSIM (The Agricultural Production Systems sIMulator), was used to simulate root-zone soil water content for a study field in south-eastern Australia. Through the simulation, we evaluated different irrigation scheduling decisions using ensemble short-term rainfall forecasts. This modelling produced an ensemble of simulations of soil water content, as well as ensemble simulations of irrigation runoff and drainage. This enabled quantification of risks of over- and under-irrigation. These ensemble estimates were interpreted to inform the timing of the next irrigation event to minimize both the risks of stressing the crop and/or wasting water under uncertain future weather. With extension to include other sources of uncertainty (e.g., evapotranspiration forecasts, crop coefficient), we plan to build a comprehensive uncertainty framework to support on-farm irrigation decision-making.
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ItemMulti-scale analysis of bias correction of soil moisture( 2014-07-29)Abstract. Remote sensing, in situ networks and models are now providing unprecedented information for environmental monitoring. To conjunctively use multi-source data nominally representing an identical variable, one must resolve biases existing between these disparate sources, and the characteristics of the biases can be non-trivial due to spatiotemporal variability of the target variable, inter-sensor differences with variable measurement supports. One such example is of soil moisture (SM) monitoring. Triple collocation (TC) based bias correction is a powerful statistical method that increasingly being used to address this issue but is only applicable to the linear regime, whereas nonlinear method of statistical moment matching is susceptible to unintended biases originating from measurement error. Since different physical processes that influence SM dynamics may be distinguishable by their characteristic spatiotemporal scales, we propose a multi-time-scale linear bias model in the framework of a wavelet-based multi-resolution analysis (MRA). The joint MRA-TC analysis was applied to demonstrate scale-dependent biases between in situ, remotely-sensed and modelled SM, the influence of various prospective bias correction schemes on these biases, and lastly to enable multi-scale bias correction and data adaptive, nonlinear de-noising via wavelet thresholding.