Search results for: Kathleen M. Curran

Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer

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Model assessment, in the Bayesian context, involves evaluation of the goodness-of-fit and the comparison of several alternative candidate models for predictive accuracy and improvements. In posterior predictive checks, the data simulated under the fitted model is compared with the actual data. Predictive model accuracy is estimated using information criteria such as the Akaike information criterion (AIC), the Bayesian information criterion (BIC), the Deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). The goal of an information criterion is to obtain an unbiased measure of out-of-sample prediction error. Since posterior checks use the data twice; once for model estimation and once for testing, a bias correction which penalises the model complexity is incorporated in these criteria. Cross-validation (CV) is another method used for examining out-of-sample prediction accuracy. Leave-one-out cross-validation (LOO-CV) is the most computationally expensive variant among the other CV methods, as it fits as many models as the number of observations. Importance sampling (IS), truncated importance sampling (TIS) and Pareto-smoothed importance sampling (PSIS) are generally used as approximations to the exact LOO-CV and utilise the existing MCMC results avoiding expensive computational issues. The reciprocals of the predictive densities calculated over posterior draws for each observation are treated as the raw importance weights. These are in turn used to calculate the approximate LOO-CV of the observation as a weighted average of posterior densities. In IS-LOO, the raw weights are directly used. In contrast, the larger weights are replaced by their modified truncated weights in calculating TIS-LOO and PSIS-LOO. Although, information criteria and LOO-CV are unable to reflect the goodness-of-fit in absolute sense, the differences can be used to measure the relative performance of the models of interest. However, the use of these measures is only valid under specific circumstances. This study has developed 11 models using normal, log-normal, gamma, and student’s t distributions to improve the PCR stutter prediction with forensic data. These models are comprised of four with profile-wide variances, four with locus specific variances, and three which are two-component mixture models. The mean stutter ratio in each model is modeled as a locus specific simple linear regression against a feature of the alleles under study known as the longest uninterrupted sequence (LUS). The use of AIC, BIC, DIC, and WAIC in model comparison has some practical limitations. Even though, IS-LOO, TIS-LOO, and PSIS-LOO are considered to be approximations of the exact LOO-CV, the study observed some drastic deviations in the results. However, there are some interesting relationships among the logarithms of pointwise predictive densities (lppd) calculated under WAIC and the LOO approximation methods. The estimated overall lppd is a relative measure that reflects the overall goodness-of-fit of the model. Parallel log-likelihood profiles for the models conditional on equal posterior variances in lppds were observed. This study illustrates the limitations of the information criteria in practical model comparison problems. In addition, the relationships among LOO-CV approximation methods and WAIC with their limitations are discussed. Finally, useful recommendations that may help in practical model comparisons with these methods are provided.

Keywords: cross-validation, importance sampling, information criteria, predictive accuracy

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Authors: Asfaw Gezae Daful, Mohsen Alimandagari, Kathleen Haigh, Somayeh Farzad, Eugene Van Rensburg, Johann F. Görgens

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The sugar industry has to 're-invent' itself to ensure long-term economic survival and opportunities for job creation and enhanced community-level impacts, given increasing pressure from fluctuating and low global sugar prices, increasing energy prices and sustainability demands. We propose biorefineries for re-vitalisation of the sugar industry using low value lignocellulosic biomass (sugarcane bagasse, leaves, and tops) annexed to existing sugar mills, producing a spectrum of high value platform chemicals along with biofuel, bioenergy, and electricity. Opportunity is presented for greener products, to mitigate climate change and overcome economic challenges. Xylose from labile hemicellulose remains largely underutilized and the conversion to value-add products a major challenge. Insight is required on pretreatment and/or extraction to optimize production of cellulosic ethanol together with lactic acid, furfural or biopolymers from sugarcane bagasse, leaves, and tops. Experimental conditions for alkaline and pressurized hot water extraction dilute acid and steam explosion pretreatment of sugarcane bagasse and harvest residues were investigated to serve as a basis for developing various process scenarios under a sugarcane biorefinery scheme. Dilute acid and steam explosion pretreatment were optimized for maximum hemicellulose recovery, combined sugar yield and solids digestibility. An optimal range of conditions for alkaline and liquid hot water extraction of hemicellulosic biopolymers, as well as conditions for acceptable enzymatic digestibility of the solid residue, after such extraction was established. Using data from the above, a series of energy efficient biorefinery scenarios are under development and modeled using Aspen Plus® software, to simulate potential factories to better understand the biorefinery processes and estimate the CAPEX and OPEX, environmental impacts, and overall viability. Rigorous and detailed sustainability assessment methodology was formulated to address all pillars of sustainability. This work is ongoing and to date, models have been developed for some of the processes which can ultimately be combined into biorefinery scenarios. This will allow systematic comparison of a series of biorefinery scenarios to assess the potential to reduce negative impacts on and maximize the benefits of social, economic, and environmental factors on a lifecycle basis.

Keywords: biomass, biorefinery, green economy, sustainability

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Authors: Anil K. Giri, Dipak Subedi, Kathleen Kassel, Ashok Mishra

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The United States Department of Agriculture’s programs has been accused of being discriminatory in the past based on the race of the farmer, especially African-American producers. This study examines if there was racial discrimination in payments from the most recent new USDA programs, including those made in response to the pandemic. This study uses the Analysis of Variance (ANOVA) to examine the payments after normalizing them relative to cash receipts to test if discrimination in the number of payments received exists. Three programs investigated in this study are: i) the Coronavirus Food Assistance Program (CFAP), ii) the Market Facilitation Program (MFP), and (iii) the Paycheck Protection Program (PPP). The PPP program was administered by the Small Business Administration, whereas the other two were designed and implemented by the USDA. The PPP made forgivable loans to small businesses and, initially, was heavily criticized for not reaching minority businesses (in general). The Small Business Administration then initiated a second draw of PPP loans, prioritizing minority-owned businesses. This study compares attributes of PPP loans made to African-American farming businesses and other farming businesses in the two draws of the PPP. We find that the number of African-American farming businesses participating in the second draw of PPP loans decreased significantly from the first draw. However, the average amount of PPP loans to African-American farming businesses increased in the second draw. In the first draw, the average cost of jobs reported per loan was higher for African-American farming businesses than for other producers. In the second draw, the average cost of jobs reported per loan was significantly higher for other farming businesses than for African-American businesses. The share of PPP loans forgiven for African-American farming businesses is significantly below the national rate of 89 percent. The rate of forgiveness for PPP loans made to African-American producers is unlikely to increase significantly without policy changes. This can increase financial burdens in the future to farm operations operated by African- Americans. Finally, we conclude that the initial goal of increasing minority participation in PPP loans in the second draw, at least among African-Americans in the agricultural sector, did not meet. CFAP made almost $600 million in direct payments to minority producers, including Black producers. Black or African American producers received more than $52 million in CFAP payments. CFAP payments were proportional to the value of agricultural commodities sold for most minority producers. The 2017 Census of Agriculture showed that the majority of minority producers, including African American producers but excluding Asian producers, raised livestock. CFAP made the highest payments to livestock minority producers.

Keywords: United States department of agriculture (USDA), coronavirus food assistance program (CFAP), paycheck protection program (PPP), African-American producers, minority American producers

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Authors: Ali A Alshraifeen, Josie Evans, Kathleen Stoddart

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End-stage renal disease (ESRD) introduces physical, psychological, social, emotional and spiritual challenges into patients’ lives. Spirituality has been found to contribute to improved health outcomes, mainly in the areas of quality of life (QOL) and well-being. No studies exist to explore the influence of spirituality on the health outcomes and general well-being in patients with end-stage renal disease receiving hemodialysis (HD) treatment in Scotland. This study was conducted to explore spirituality in the daily lives of among these patients and how it may influence their QOL and general well-being. The study employed a qualitative method. Data were collected using semi-structured interviews with a sample of 21 patients. A thematic approach using Framework Analysis informed the qualitative data analysis. Participants were recruited from 11 dialysis units across four Health Boards in Scotland. The participants were regular patients attending the dialysis units three times per week. Four main themes emerged from the qualitative interviews: ‘Emotional and Psychological Turmoil’, ‘Life is Restricted’, ‘Spirituality’ and ‘Other Coping Strategies’. The findings suggest that patients’ QOL might be affected because of the physical challenges such as unremitting fatigue, disease unpredictability and being tied down to a dialysis machine, or the emotional and psychological challenges imposed by the disease into their lives such as wholesale changes, dialysis as a forced choice and having a sense of indebtedness. The findings also revealed that spirituality was an important coping strategy for the majority of participants who took part in the qualitative component (n=16). Different meanings of spirituality were identified including connection with God or Supernatural Being, connection with the self, others and nature/environment. Spirituality encouraged participants to accept their disease and offered them a sense of protection, instilled hope in them and helped them to maintain a positive attitude to carry on with their daily lives, which may have had a positive influence on their health outcomes and general well-being. The findings also revealed that humor was another coping strategy that helped to diffuse stress and anxiety for some participants and encouraged them to carry on with their lives. The findings from this study provide a significant contribution to a very limited body of work. The study contributes to our understanding of spirituality and how people receiving dialysis treatment use it to manage their daily lives. Spirituality is of particular interest due to its connection with health outcomes in patients with chronic illnesses. The link between spirituality and many chronic illnesses has gained some recognition, yet the identification of its influence on the health outcomes and well-being in patients with ESRD is still evolving. There is a need to understand patients’ experiences and examine the factors that influence their QOL and well-being to ensure that the services available are adequately tailored to them. Hence, further research is required to obtain a better understanding of the influence of spirituality on the health outcomes and general well-being of patients with ESRD.

Keywords: end-stage renal disease, general well-being, quality of life, spirituality

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Authors: Kathleen Frances Haigh, Mieke Nieder-Heitmann, Somayeh Farzad, Mohsen Ali Mandegari, Johann Ferdinand Gorgens

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Lignocellulose can be converted to a range of biochemicals and biofuels. Where this is derived from agricultural waste, issues of competition with food are virtually eliminated. One such source of lignocellulose is the South African sugar industry. Lignocellulose could be accessed by changes to the current farming practices and investments in more efficient boilers. The South African sugar industry is struggling due to falling sugar prices and increasing costs and it is proposed that annexing a biorefinery to a sugar mill will broaden the product range and improve viability. Process simulations of the selected chemicals were generated using Aspen Plus®. It was envisaged that a biorefinery would be annexed to a typical South African sugar mill. Bagasse would be diverted from the existing boilers to the biorefinery and mixed with harvest residues. This biomass would provide the feedstock for the biorefinery and the process energy for the biorefinery and sugar mill. Thus, in all scenarios a portion of the biomass was diverted to a new efficient combined heat and power plant (CHP). The Aspen Plus® simulations provided the mass and energy balance data to carry out an economic assessment of each scenarios. The net present value (NPV), internal rate of return (IRR) and minimum selling price (MSP) was calculated for each scenario. As a starting point scenarios were generated to investigate the production of ethanol, ethanol and lactic acid, ethanol and furfural, butanol, methanol, and Fischer-Tropsch syncrude. The bypass to the CHP plant is a useful indicator of the energy demands of the chemical processes. An iterative approach was used to identify a suitable bypass because increasing this value had the combined effect of increasing the amount of energy available and reducing the capacity of the chemical plant. Bypass values ranged from 30% for syncrude production to 50% for combined ethanol and furfural production. A hurdle rate of 15.7% was selected for the IRR. The butanol, combined ethanol and furfural, or the Fischer-Tropsch syncrude scenarios are unsuitable for investment with IRRs of 4.8%, 7.5% and 11.5% respectively. This provides valuable insights into research opportunities. For example furfural from sugarcane bagasse is an established process although the integration of furfural production with ethanol is less well understood. The IRR for the ethanol scenario was 14.7%, which is below the investment criteria, but given the technological maturity it may still be considered for investment. The scenarios which met the investment criteria were the combined ethanol and lactic acid, and the methanol scenarios with IRRs of 20.5% and 16.7%, respectively. These assessments show that the production of biochemicals from lignocellulose can be commercially viable. In addition, this assessment have provided valuable insights for research to improve the commercial viability of additional chemicals and scenarios. This has led to further assessments of the production of itaconic acid, succinic acid, citric acid, xylitol, polyhydroxybutyrate, polyethylene, glucaric acid and glutamic acid.

Keywords: biorefineries, sugar mill, methanol, ethanol

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Authors: Jong H. Kim, Kathleen L. Chan, Luisa W. Cheng

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Control of fungal pathogens, such as foodborne mycotoxin producers, is problematic as effective antimycotic agents are often very limited. Mycotoxin contamination significantly interferes with the safe production of foods or crops worldwide. Moreover, expansion of fungal resistance to commercial drugs or fungicides is a global human health concern. Therefore, there is a persistent need to enhance the efficacy of commercial antimycotic agents or to develop new intervention strategies. Disruption of the cellular antioxidant system should be an effective method for pathogen control. Such disruption can be achieved with safe, redox-active compounds. Natural phenolic derivatives are potent redox cyclers that inhibit fungal growth through destabilization of the cellular antioxidant system. The goal of this study is to identify novel, redox-active compounds that disrupt the fungal antioxidant system. The identified compounds could also function as sensitizing agents to conventional antimycotics (i.e., chemosensitization) to improve antifungal efficacy. Various benzo derivatives were tested against fungal pathogens. Gene deletion mutants of the yeast Saccharomyces cerevisiae were used as model systems for identifying molecular targets of benzo analogs. The efficacy of identified compounds as potent antifungal agents or as chemosensitizing agents to commercial drugs or fungicides was examined with methods outlined by the Clinical Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing. Selected benzo derivatives possessed potent antifungal or antimycotoxigenic activity. Molecular analyses by using S. cerevisiae mutants indicated antifungal activity of benzo derivatives was through disruption of cellular antioxidant or cell wall integrity system. Certain benzo analogs screened overcame tolerance of Aspergillus signaling mutants, namely mitogen-activated protein kinase mutants, to fludioxonil fungicide. Synergistic antifungal chemosensitization greatly lowered minimum inhibitory or fungicidal concentrations of test compounds, including inhibitors of mitochondrial respiration. Of note, salicylaldehyde is a potent antimycotic volatile that has some practical application as a fumigant. Altogether, benzo derivatives targeting cellular antioxidant system of fungi (along with cell wall integrity system) effectively suppress fungal growth. Candidate compounds possess the antifungal, antimycotoxigenic or chemosensitizing capacity to augment the efficacy of commercial antifungals. Therefore, chemogenetic approaches can lead to the development of novel antifungal intervention strategies, which enhance the efficacy of established microbe intervention practices and overcome drug/fungicide resistance. Chemosensitization further reduces costs and alleviates negative side effects associated with current antifungal treatments.

Keywords: antifungals, antioxidant system, benzo derivatives, chemosensitization

Procedia PDF Downloads 259