Return and Efficiency of Intercropped Pineapple Cultivation in Kerala

School of management studies

Soft Computing Approach for Optimization of siRNA Efficiency Prediction for Post-transcriptional Gene Silencing

Post-transcriptional gene silencing by RNA interference is mediated by small interfering RNA called siRNA. This gene silencing mechanism can be exploited therapeutically to a wide variety of disease-associated targets, especially in AIDS, neurodegenerative diseases, cholesterol and cancer on mice with the hope of extending these approaches to treat humans. Over the recent past, a significant amount of work has been undertaken to understand the gene silencing mediated by exogenous siRNA. The design of efficient exogenous siRNA sequences is challenging because of many issues related to siRNA. While designing efficient siRNA, target mRNAs must be selected such that their corresponding siRNAs are likely to be efficient against that target and unlikely to accidentally silence other transcripts due to sequence similarity. So before doing gene silencing by siRNAs, it is essential to analyze their off-target effects in addition to their inhibition efficiency against a particular target. Hence designing exogenous siRNA with good knock-down efficiency and target specificity is an area of concern to be addressed. Some methods have been developed already by considering both inhibition efficiency and off-target possibility of siRNA against agene. Out of these methods, only a few have achieved good inhibition efficiency, specificity and sensitivity. The main focus of this thesis is to develop computational methods to optimize the efficiency of siRNA in terms of “inhibition capacity and off-target possibility” against target mRNAs with improved efficacy, which may be useful in the area of gene silencing and drug design for tumor development. This study aims to investigate the currently available siRNA prediction approaches and to devise a better computational approach to tackle the problem of siRNA efficacy by inhibition capacity and off-target possibility. The strength and limitations of the available approaches are investigated and taken into consideration for making improved solution. Thus the approaches proposed in this study extend some of the good scoring previous state of the art techniques by incorporating machine learning and statistical approaches and thermodynamic features like whole stacking energy to improve the prediction accuracy, inhibition efficiency, sensitivity and specificity. Here, we propose one Support Vector Machine (SVM) model, and two Artificial Neural Network (ANN) models for siRNA efficiency prediction. In SVM model, the classification property is used to classify whether the siRNA is efficient or inefficient in silencing a target gene. The first ANNmodel, named siRNA Designer, is used for optimizing the inhibition efficiency of siRNA against target genes. The second ANN model, named Optimized siRNA Designer, OpsiD, produces efficient siRNAs with high inhibition efficiency to degrade target genes with improved sensitivity-specificity, and identifies the off-target knockdown possibility of siRNA against non-target genes. The models are trained and tested against a large data set of siRNA sequences. The validations are conducted using Pearson Correlation Coefficient, Mathews Correlation Coefficient, Receiver Operating Characteristic analysis, Accuracy of prediction, Sensitivity and Specificity. It is found that the approach, OpsiD, is capable of predicting the inhibition capacity of siRNA against a target mRNA with improved results over the state of the art techniques. Also we are able to understand the influence of whole stacking energy on efficiency of siRNA. The model is further improved by including the ability to identify the “off-target possibility” of predicted siRNA on non-target genes. Thus the proposed model, OpsiD, can predict optimized siRNA by considering both “inhibition efficiency on target genes and off-target possibility on non-target genes”, with improved inhibition efficiency, specificity and sensitivity. Since we have taken efforts to optimize the siRNA efficacy in terms of “inhibition efficiency and offtarget possibility”, we hope that the risk of “off-target effect” while doing gene silencing in various bioinformatics fields can be overcome to a great extent. These findings may provide new insights into cancer diagnosis, prognosis and therapy by gene silencing. The approach may be found useful for designing exogenous siRNA for therapeutic applications and gene silencing techniques in different areas of bioinformatics.

Nutrient cycling and nutrient use efficiency in urban and peri-urban agriculture of Kabul, Afghanistan

Like elsewhere also in Kabul, Afghanistan urban and peri-urban agriculture (UPA) has often been accused of being resource inefficient and unsustainable causing negatives externalities to community health and to the surroundings. These arise from the inappropriate management and use of agricultural inputs, including often pesticides and inter-city wastes containing heavy metal residues and pathogens. To address these concerns, parallel studies with the aims of quantification of carbon (C), nitrogen (N), phosphorus (P) and potassium (K) horizontal and vertical fluxes; the assessment of heavy metal and pathogen contaminations of UPA produce, and an economic analysis of cereal, vegetable and grape production systems conducted for two years in UPA of Kabul from April 2008 to October 2009. The results of the studies from these three UPA diverse production systems can be abridged as follows: Biennial net balances in vegetable production systems were positive for N (80 kg ha-1 ), P (75 kg ha-1) and C (3,927 kg ha-1), negative for K (-205 kg ha-1), whereas in cereal production systems biennial horizontal balances were positive for P (20 kg ha-1 ) and C (4,900 kg ha-1) negative for N (-155 kg ha-1) and K (-355 kg ha-1) and in vineyards corresponding values were highly positive for N (295 kg ha-1), P (235 kg ha-1), C (3,362 kg ha-1) and slightly positive for K (5 kg ha-1). Regardless of N and C gaseous emissions, yearly leaching losses of N and P in selected vegetable gardens varied from 70 - 205 kg N ha-1 and 5 - 10 kg P ha-1. Manure and irrigation water contributed on average 12 - 79% to total Inputs of N, P, K and C, 10 - 53% to total inputs of C in the gardens and fields. The elevated levels of heavy metal and pathogen loads on fresh UPA vegetables reflected contamination from increasing traffic in the city, deposits of the past decades of war, lacking collection and treatment of raw inter-city wastes which call for solutions to protect consumer and producer health and increase reliability of UPA productions. A cost-revenue analysis of all inputs and outputs of cereal, vegetable and grapes production systems over two years showed substantial differences in net UPA household income. To confirm these results, more detailed studies are needed, but tailoring and managing the optimal application of inputs to crop needs will significantly enhance farmer’s better revenues as will as environmental and produce quality.

Technical and scale efficiency of cassava production system in Delta State, Nigeria: an application of Two-Stage DEA approach

The present study examines the level of pure technical and scale efficiencies of cassava production system including its sub-processes (that is production and processing stages) of 278 cassava farmers/processors from three regions of Delta State, Nigeria by applying Two-Stage Data Envelopment Analysis (DEA) approach. Results reveal that pure technical efficiency (PTE) is significantly lower at the production stage 0.41 vs 0.55 for the processing stage, but scale efficiency (SE) is high at both stages (0.84 and 0.87), implying that productivity can be improved substantially by reallocation of resources and adjusting operation size. The socio-economic determinants exert differential impacts on PTE and SE at each stage. Overall, education, experience and main occupation as farmer significantly improve SE while subsistence pressure reduces it. Extension contact significantly improves SE at the processing stage but reduces PTE and SE overall. Inverse size-PTE and size-SE relationships exist in cassava production system. In other words, large/medium farms are technically and scale inefficient. Gender gap exists in performance. Male farmers are technically efficient at processing stage but scale inefficient overall. Farmers in northern region are technically efficient. Investments in education, extension services and infrastructure are suggested as policy options to improve the cassava sector in Nigeria.

Determinants of technical efficiency of freshwater prawn farming in southwestern Bangladesh

This paper estimates a translog stochastic production function to examine the determinants of technical efficiency of freshwater prawn farming in Bangladesh. Primary data has been collected using random sampling from 90 farmers of three villages in southwestern Bangladesh. Prawn farming displayed much variability in technical efficiency ranging from 9.50 to 99.94% with mean technical efficiency of 65%, which suggested a substantial 35% of potential output can be recovered by removing inefficiency. For a land scarce country like Bangladesh this gain could help increase income and ensure better livelihood for the farmers. Based on the translog production function specification, farmers could be made scale efficient by providing more input to produce more output. The results suggest that farmers’ education and non-farm income significantly improve efficiency whilst farmers’ training, farm distance from the water canal and involvement in fish farm associations reduces efficiency. Hence, the study proposes strategies such as less involvement in farming-related associations and raising the effective training facilities of the farmers as beneficial adjustments for reducing inefficiency. Moreover, the key policy implication of the analysis is that investment in primary education would greatly improve technical efficiency.

The efficiency of direct payments versus tax reductions under uncertainty

This paper analyzes the optimal behavior of farmers in the presence of direct payments and uncertainty. In an empirical analysis for Switzerland, it confirms previously obtained theoretical results and determines the magnitude of the theoretical predicted effects. The results show that direct payments increase agricultural production between 3.7% to 4.8%. Alternatively to direct payments, the production effect of tax reductions is evaluated in order to determine its magnitude. The empirical analysis corroborates the theoretical results of the literature and demonstrates that tax reductions are also distorting, but to a substantially lesser degree if losses are not offset. However, tax reductions, independently whether losses are offset or not, lead to higher government spending than pure direct payments

Bilateral trade between New Zealand & the pacific alliance: perspectives and possibilities for further trade engagement

Due to the rapid and effective success of countries in the Pacific Rim for the last two decades, current world trade attention has been focussed on what appears to be the common vision of the ‘Pacific Century’. Reducing attention from the Atlantic and focusing it on the Pacific represents a new challenge for countries touching this ocean. The main Latin American economies bordering the pacific have taken upon this challenge with the creation of the Pacific Alliance in 2011. In this way, Chile, Colombia, Mexico and Peru intend to penetrate and increase trade with the region by forming a coalition. The Pacific Alliance has attracted international attention, interest and support from nations around the world, counting 32 countries as observers; 7 are actually located in the region and six of them rank amongst the Top 15 world economies. As is expected, the possibility of closer trade engagement with big players such as China, India, Japan, South Korea or Australia absorb the main attention of media, governments and academics alike, leaving behind other feasible and possible opportunities unattended. That is precisely the case of New Zealand and its favourable commerce opportunities with the Pacific Alliance. The following document will study the major trends and variations in trade between New Zealand, the Pacific Alliance and its members between 2010 and 2014. Proving that mutual trade is most likely to keep on growing.