SPsimSeq : semi-parametric simulation of bulk and single-cell RNA-sequencing data

SPsimSeq is a semi-parametric simulation method to generate bulk and single-cell RNA-sequencing data. It is designed to simulate gene expression data with maximal retention of the characteristics of real data. It is reasonably flexible to accommodate a wide range of experimental scenarios, including different sample sizes, biological signals (differential expression) and confounding batch effects

Review of Mango Value Chain in Ethiopia

Mango is one of the main fruit crop produced and exported in Ethiopia. The main objective of this review is to review mango production and marketing system with their respective constraints, to identify major actors along mango value chain and their respective functions along the chain and to review current status and potential opportunities of mango in Ethiopian economy. Accordingly, using of small scale irrigation, fertilizer application, use of farm yard manure, intercropping with other crops and mixed farming systems are the main mango production practices adopted in different parts of the country. In line with this, the main constraints of mango production are mentioned as irrigation water scarcity, pest and disease and technology limitation, limited access to mango varieties, and limited capacity in R&D.  Marketing system of mango in Ethiopia is characterized by use of traditional transportation means such as donkeys, cart, human back and marketing is mainly oriented on local market. The main constraints of mango marketing are mentioned as lack of markets to absorb the production, low price for the products, poor product handling and packaging, imperfect pricing system and lack of transparency in market information system mainly in the export market. The main factors involved along mango value chain are input suppliers, producers, collectors, wholesalers, retailers and processors. Currently, mango sub-sector is a good entry point for tackling poverty and that the market for mangoes in Ethiopia is significant and growing. Distribution of pest and disease resistance and early maturing varieties is a method to increase production potential. Facilities like road, canal and transportation system should be improved for further dimension and to reduce the loss. Keywords: mango, value chain, production constraints, spatial marke

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Background: In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost of data generation as well as the statistical power for differential gene expression (DGE) analysis. For RNA sequencing, with its different quantitative output in terms of counts and tunable dynamic range, the adequacy and empirical validation of RNA sample pooling strategies have not yet been evaluated. In this study, we comprehensively assessed the utility of pooling strategies in RNA-seq experiments using empirical and simulated RNA-seq datasets. Result: The data generating model in pooled experiments is defined mathematically to evaluate the mean and variability of gene expression estimates. The model is further used to examine the trade-off between the statistical power of testing for DGE and the data generating costs. Empirical assessment of pooling strategies is done through analysis of RNA-seq datasets under various pooling and non-pooling experimental settings. Simulation study is also used to rank experimental scenarios with respect to the rate of false and true discoveries in DGE analysis. The results demonstrate that pooling strategies in RNA-seq studies can be both cost-effective and powerful when the number of pools, pool size and sequencing depth are optimally defined. Conclusion: For high within-group gene expression variability, small RNA sample pools are effective to reduce the variability and compensate for the loss of the number of replicates. Unlike the typical cost-saving strategies, such as reducing sequencing depth or number of RNA samples (replicates), an adequate pooling strategy is effective in maintaining the power of testing DGE for genes with low to medium abundance levels, along with a substantial reduction of the total cost of the experiment. In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize the cost and maintain the power

Ethnobotanical Study of Medicinal Plants in Wolaita Zone, Southern Ethiopia

The aim of this study is to investigate medicinal plant diversity, ethnobotanical study and to document indigenous knowledge of people in wolaita zone. Data were gathered from, local healers using different ethnobotanical techniques such as; semi- structured interview, field observation, and group discussion & analyzed using descriptive statistical analysis methods. Discussions were conducted with informants and residents in seeking to understand the use, threats to traditional medicinal plants and its management, and to know how knowledge is maintained and transferred through family or community. A total of 60 traditional healers (40 men and 20 women) from the age of 18 and above were selected purposefully based on their knowledge and practice on medicinal plants. A total of 102 medicinal plant species belonging to 100 genera and 54 families were collected from the study area, among them 76(74.5%), were collected from wild while the remained 26(25.49%), were cultivated in the homegardens. The Family lamiaceae contributed the highest number of medicinal plants 12(11.8%), followed by Astraceae 8(7.84%).Based on the growth forms herbs accounted the highest numbers(49%).Regarding plant parts used  leaves were the most frequently sought plant parts accounting for (66%). Majority of remedies (52%) were applied in mixing with pure water and (31%) used alone. Of the total medicinal plant species reported, 84% and 9.8% were used to treat human and livestock ailments respectively. The remained 5.9% were used to against both human and livestock ailments. Greater proportion of rout of administration 80%, were oral. Analysis of preference ranking showed, Ajuga integrifolia was the most perceived & preferred medicinal plant by people of the study area to treat stomach ache. Stepania abyssinica was found to be the most preferred plant to treat stomach complains in livestock. Some medicinal plants are popular than others in treating various diseases. For instance, Allium sativum were found to be the most popular, followed by Moringa stenopetala treating malaria. Concerning informant consensus factor, the highest ICF values were linked to problems associated with stomach ache (0.71). Jaccard`s Coefficient of Similarity (JCS) revealed highest similarity 34% were, found b/n sidama. Youngsters have almost no aims to receive and to transfer medicinal plant knowledge, so concerning bodies to create awareness in the area suggested. Agricultural expansion, were reported to be the major pressure to medicinal plants & little practice of conservation measures in the area. Keywords: Indigenous knowledge, ethinobotany and use categories, ailments, conservation & threats

Consequence of Inter and Intra-Row Spacing on Growth and Yield Components of Potato (SolaniumTubersom L.) under Irrigation at North Shewa Zone of Oromia Region, Ethiopia

Lack of production practices have been the major bottleneck of potato production and productivities in oromia, particularly at Fitche area. Since there have been no recommended inter and intra row spacing, farmers used to practice non-uniform plant spacing. Thus, a field experiment was conducted to investigate the influence of intra and inter row spacing   on growth and yield parameters of potato, thereby to recommended the optimum intra and inter row spacing  practices to farmers in the study area. The study was conducted between August 2015 and April 2016 at Fitchearea(Addis Ababa university  Salalecampus, demonstration field).Four different intra and inter row spacing's (60*20, 60*25, 60*30,70*20,70*25,70*30,80*20,80*25 and 80*30) were evaluated using  one variety of potato (Managasha) laid out in randomized complete block design replicated three times. Data on growth and yield parameters were recorded and subjected to analysis of variance (ANOVA). Results indicated that inter  and intra  row spacing  of  80*30 was superior in growth parameters such as, days to 50% flowering,days to 70% maturity, stem diameter, main stem number, plant height. Mean tuber no. count hill-1, Total tuber yield (t/ha), Marketable tuber yield(t/ha), were better at wider intra and inter row spacing (80*30).But Un marketable tuber yield(t/ha) was superior at closest inter and intra row spacing (60*20).The 80*30 intra and inter row spacing is recommended for the growers of potato plant. Keywords:-Inter and intra row spacing, North shewa Zone, potato

Determinants of Rice Production and Marketing in Low Producer Farmers: The Case of Fogera Districts, North-Western Ethiopia

Ethiopia is emerging as an important rice growing country in Eastern Africa.  However, there are several constraints which drastically affect rice production and its marketing system under smallholder farmer’s condition. This study aimed at examining the socioeconomic determinants of rice production and marketing in low producer farmers in the study area. A sample of 160 rice producer and 50 traders were interviewed using structured questionnaire. The result of the study showed that sex of household head is positive and statically significant in explaining rice production at 5% significant level (p<0.05). Oxen ownership (p<0.07) and land size (P<0.067) were directly proportional to rice production and significant at 10% level of significance respectively. Moreover, labor availability and   rice seed rate was highly significant at 1% level of significance (p<0.001).  It is  recommended that farmers should  use intensive farming by increasing productivity of the land using improved varities, application of other alternative traction power(oxen) , adopting labor saving technology and management of seed rate (agronomic practices)during sowing .  Moreover, there is a need to consider gender differentials in rice production system. The S-C-P- model reflects that the structure of rice marketing is imperfect market (oligopsonistic), only few buyers governed the market. The Gross marketing margin indicated that assemblers harvest the highest marketing margin as compare to other market participants and farmers received below the total average share of the margin.  High investment capital, and competition with unlicensed traders were the barrier in rice marketing. Hence, facilitating loan (credit services), increasing the bargaining power farmers & licensing illegal traders were the recommendation forwarded. Keywords: Rice, marketing, concentration ratio, S-C-P model, Ethiopia

Development Of A Real-Time Pcr Assay For Diagnosis Of Brucella Melitensis Infection In Sheep

In this study, a SYBR Green based real-time PCR assay using primers specific to IS711 of Brucella melitensis was developed and its diagnostic utility was evaluated by comparing it with conventional PCR method for detection of Brucella DNA from cultured bacteria and experimentally infected mice samples. The study was first undertaken with cultured bacteria, B. melitensis 16M as a reference and two B. melitensis Malysian isolates. Brucella abortus 544 and Yersinia enterocolitica O:9 were also used for cross reactivity testing. Three of the B. melitensis were successfully detected using both optimized SYBR Green I real-time and conventional PCR. No amplification products were produced with these primers from strains of B. abortus and Y. enterocolitica O:9 indicating that the primer sets are specific only for B. melitensis. The specificity of the PCR products amplified by the primers from Malysian strains of B. melitensis were confirmed by sequence analysis. The detection limit of the real-time PCR was compared with conventional PCR by preparing serially ten-fold dilutions of B.melitensis DNA. The real-time PCR was found to be 10-fold more sensitive than the conventional PCR, detecting up to 50 fg of genomic DNA. The viability of using conventional and real-time PCR assays together with culture methods as potential diagnostic tools for the detection of B. melitensis in experimentally infected mice was also assessed over an 8-week period of infection. It was evident from our result that regardless of duration of infection and sample type (liver, lymph node, blood, spleen and serum) the diagnostic yield (sensitivity) was 100%, 96.7% and 62.5% for real-time PCR, conventional PCR and culture methods respectively. This indicated that the sensitivity of the PCR assays was far higher than that of the culture method. The specificity of both conventional and real-time PCR was 100%. When serum was used as PCR template, B. melitensis specific amplicon was detected only until day 45 post inoculation (p.i) using conventional PCR unlike the real-time PCR method whereby positive results were detected through out the study period. In all samples with positive real-time PCR results, B. melitensis specific amplicons were distinguished by their characteristic melting temperature ranged between 86.4 oC to 87.4 oC in melting curve analysis. Analytical sensitivities of the different tissue types used in the study were also compared using threshold cycle (Ct) values of the real-time PCR. For this purpose, samples collected at day 30 p.i. were used and the most sensitive tissue sample amongst the tested samples was estimated from the standard curve obtained from cloned B. melitensis 16M. Accordingly, the most sensitive tissue was found to be serum (mean Ct=15.07) followed by lymph node (mean Ct=19.50), spleen (mean Ct= 24.2), liver (mean Ct=26.4) and whole blood (mean Ct=26.2). These results indicate that serum samples followed by lymph node are more sensitive for the real-time PCR assay than the other samples tested in this study. In conclusion, this present results suggest that the diagnostic yield of real-time PCR that uses serum samples was at least as sensitive as a similar PCR protocol that uses other tested tissue samples. The speed and technical simplicity of real-time PCR coupled with minimal risk of handling serum samples make it a useful alternative to blood / other tested tissue PCR for animals with suspected brucellosis and negative or doubtful serological test results. However, although the use of this real-time PCR assay as a supplemental diagnostic tool for detection and identification of Brucella organisms in clinical specimens could be recommended, the need for the assay to be validated with confirmed positive and negative clinical samples of its primary host animals, and verify its ability to differentiate the vaccinal strains from field strains, is desirable to achieve the utmost benefits from the SYBR Green I based real-time PCR assay

Determinants of Cereal Crops Productivity: In Case of Kecha Birra Woreda, Snnpr, Ethiopia

This study conducted to investigate the determinants of cereal crop productivity of small household farmers in southern region, a case of Kecha Birra woreda.To study the determinants of cereal crop productivity descriptive and econometrics analysis was carried out, a positive increasing trend was found in agricultural productivity and data collection was from rural household farmers selected through random sampling techniques for the collected cross-sectional data on 100 samples of the farmers at household level.  Agriculture plays prominent role in the process of economic development for a country. Without achieving substantial increase in agricultural production, no country has moved to take off stage of economic development. The general objective of the study is to assess the determinants of cereal crop productivity in Kecha Birra Woreda. The study found that improved seed, farm size, fertilizer, education, family size, age, and irrigation have the positive effects in the productivity of cereal crops. The sex and credit have negative impact on cereal crops productivity in the study area. Since the improved seed, farm size, fertilizer, family size, credit and irrigation significantly affect the yield capacity of the cereal crops, the farmers should be encouraged in order to use them and the government should provide the access to the farmers. Keywords: Agriculture, Cereal crops, Smallholder farmers DOI: 10.7176/JESD/10-17-04 Publication date:September 30th 201

Short-run Behavior of Defensive Assets in the Ethiopian Commercial Banking Sector

The paper aims to identify and measure the impact of factors responsible in shaping the behavior of defensive assets in the Ethiopian banking sector. The focus of the analysis is on the Ethiopian banking sector rather than an individual bank. An attempt is made to capture how the Ethiopian banking sector adjusts its defensive asset position to changes in money supply, relative yields on asset holdings, discount rate, the demand for different bank assets, availability of funds, and legal reserve requirements. Except for required reserves, discount rate and relative yields on asset holdings, the rest of the explanatory variables are statistically significant in explaining the short-run behavior of defensive assets. The paper concludes initial stock of excess reserves, treasury bills, loans and their lag, narrow money supply, saving deposit of the public held with different financial institutions, and bank capital are what explain short-run behavior of defensive assets in the Ethiopian banking sector. Finally, the difference in the behavior of excess & free reserves found to be negligible which is a signal of insignificant use of short-term borrowings in the Ethiopian commercial banking system

Macroeconomic Impact of Tax Reform in Ethiopia

This study analyzes the economy wide impact of tax reform on Ethiopian economy using Dynamic Computable General Equilibrium (DCGE) model. It utilized the updated 2009/10 Ethiopian Social Accounting Matrix (SAM) from 2005/06 developed by Ethiopian Development Research Institute (EDRI). In order to investigate the impact of tax reform on Ethiopian economy different simulations were made turn by turn. First, a reduction in direct tax by 30% is introduced to see its impacts on economy. Consequently, GDP and all other macroeconomic variables such as: absorption, private consumption, government expenditure, import, export, government income, investment, and aggregate output show a considerable improvement. On the second simulation sale tax increased by 66.27% to look the impact of sales tax on economy. As a result, sale tax improve the overall economic performance by improving the government revenue compared to direct tax reduction. Under the third scenario reduction of import tariff by 24% deteriorated the overall economic performance by boosting import and discouraging domestic output. Based on the finding, inspiring direct tax reform and consumption tax reform, protecting the home country from external sector influence to encourage domestic production are the major policy option recommended to bring a good economic performance with lower distortion since it is difficult to abolish distortion when tax reform is conducted. Keywords: Ethiopia, Tax Reform, Tax Revenue, Macroeconomics performance, Dynamic Computable General Equilibrium