Parasitoid assemblage associated with a North American pine weevil in South Africa

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Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices

Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly heterogeneous. Differences in allele frequency and linkage disequilibrium patterns between the training and prediction genotypes may limit prediction accuracy. This leads to the question of whether all available data or a subset of it should be used to calibrate genomic prediction models. Previous research on training set optimization has focused on identifying a subset of the available data that is optimal for a given prediction set. However, this approach does not contemplate the possibility that different training sets may be optimal for different prediction genotypes. To address this problem, we recently introduced a sparse selection index (SSI) that identifies an optimal training set for each individual in a prediction set. Using additive genomic relationships, the SSI can provide increased accuracy relative to genomic-BLUP (GBLUP). Non-parametric genomic models using Gaussian kernels (KBLUP) have, in some cases, yielded higher prediction accuracies than standard additive models. Therefore, here we studied whether combining SSIs and kernel methods could further improve prediction accuracy when training genomic models using multi-generation data. Using four years of doubled haploid maize data from the International Maize and Wheat Improvement Center (CIMMYT), we found that when predicting grain yield the KBLUP outperformed the GBLUP, and that using SSI with additive relationships (GSSI) lead to 5–17% increases in accuracy, relative to the GBLUP. However, differences in prediction accuracy between the KBLUP and the kernel-based SSI were smaller and not always significant.Subject terms: Quantitative trait, Genetic models     

The implementation and impact of a pilot hydrocele surgery camp for LF-endemic communities in Ethiopia

BackgroundEthiopia aims to eliminate lymphatic filariasis by 2020, through a dual approach of mass drug administration to interrupt transmission and morbidity control which includes making hydrocele surgery available in all endemic areas. Locating patients requiring surgery, providing high quality surgeries, and following up patients are all formidable challenges for many resource-challenged or difficult-to-reach communities. To date, hydrocele surgery in Ethiopia has only occurred when a patient has the knowledge, time and resources to travel to regional hospitals. Ethiopia tested the novel approach of using a surgical camp, defined as mobilizing, transporting, providing surgery at a static site, and following up of a large cohort of hydrocele patients within a hospital’s catchment area, to address delays in seeking and receiving care.Methodology and resultsHealth extension workers mobilized 252 patients with scrotal swelling from a list of 385 suspected hydrocele cases from seven endemic districts in the region of Beneshangul-Gumuz. Clinical health workers and surgeons confirmed 119 as eligible for surgery. Of 70 additional patients who self-referred, 56 were eligible for surgery. Over a two-week period at a regional hospital, 175 hydrocele excision surgeries were conducted. After discharge three days after surgery, trained clinical health workers followed up with the patients on Day 5, Day 8, Day 14 and 1st-month benchmarks with a randomized follow-up of a selection of patients conducted at 9–12 months. There were no post-operative complications upon discharge at Day 3 and 22, while minor complications occurred (12.6%) between Day 3 and one month. The 9–12 month follow-up found patients self-reported an improvement in quality of life, health and economic status.ConclusionA hydrocele surgery camp was effective at providing a large number of quality surgeries in a short time. Using peripheral health workers to mobilize and follow up patients helped address delays in seeking and receiving quality care. Mainstreaming patient mobilization and follow-up into a community health system could be effective in other countries. The camp’s results also influenced two regions in Ethiopia to change their policies in order to offer free hydrocele surgery (including patient transport, consultation, surgery, diagnostic tests and necessary medications).     

Estimating number of clusters based on a general similarity matrix with application to microarray data

Many clustering methods require that the number of clusters believed present in a given data set be specified a priori, and a number of methods for estimating the number of clusters have been developed. However, the selection of the number of clusters is well recognized as a difficult and open problem and there is a need for methods which can shed light on specific aspects of the data. This paper adopts a model for clustering based on a specific structure for a similarity matrix. Publicly available gene expression data sets are analyzed to illustrate the method and the performance of our method is assessed by simulation.     

Genetic diversity in traditional Ethiopian highland maize accessions assessed by AFLP markers and morphological traits

In the highland regions of Ethiopia the heterogeneity of the land, the climate, and soil favors the presence of a large number of landraces. We analyzed a representative sample of 62 traditional Ethiopian highland maize accessions, using amplified fragment length polymorphism (AFLP^®) markers and morphological traits with the aim to group the accessions based on the their genetic profiles and morphological traits, to study agroecological variation and to assess the level of correlation between phenotypic and genetic distances. Eight EcoRI/MseI primer combinations and 15 morphological traits were used. The accessions varied significantly for all of the measured morphological traits. Of a total of 650 AFLP markers that were scored, 89.5% were polymorphic. Pair-wise genetic distance estimates based on AFLP data revealed dissimilarity coefficients ranging from 0.32 to 0.69 (mean of 0.57). Cluster analysis of the AFLP data grouped most accessions collected from the Northern highlands into one major cluster. It, however, failed to separate the Western and Southern accessions into different clusters. Regardless of the large variation in environmental conditions between agroecologies, only 9% of the total genetic variation was found between agroecologies, whereas 91% was found within agroecologies in Ethiopia. This finding may be explained by long distance seed exchange, continuous seed introduction and gene flow between agroecologies. The relationship between morphological and AFLP-based distances was significant and positive. Based on this study, three groups of highland accessions, with distinctive genetic profiles and morphological traits were identified. This information will be useful for further collections and conservation of the unique diversity included in the highland maize landraces of Ethiopia.     

Effect of Prophylactic Low Level Laser Therapy on Oral Mucositis: A Systematic Review and Meta-Analysis

Background

Objective was to determine whether prophylactic low level laser therapy (LLLT) reduces the risk of severe mucositis as compared to placebo or no therapy.

Methods

MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were searched until February 2014 for randomized controlled trials (RCTs) comparing prophylactic LLLT with placebo or no therapy in patients with cancer or undergoing hematopoietic stem cell transplantation (HSCT). All analyses used random effects models.

Results

Eighteen RCTs (1144 patients) were included. Prophylactic LLLT reduced the overall risk of severe mucositis (risk ratio (RR) 0.37, 95% confidence interval (CI) 0.20 to 0.67; P = 0.001). LLLT also reduced the following outcomes when compared to placebo/no therapy: severe mucositis at the time of anticipated maximal mucositis (RR 0.34, 95% CI 0.20 to 0.59), overall mean grade of mucositis (standardized mean difference −1.49, 95% CI −2.02 to −0.95), duration of severe mucositis (weighted mean difference −5.32, 95% CI −9.45 to −1.19) and incidence of severe pain (RR 0.26, 95% CI 0.18 to 0.37).

Conclusion

Prophylactic LLLT reduced severe mucositis and pain in patients with cancer and HSCT recipients. Future research should identify the optimal characteristics of LLLT and determine feasibility in the clinical setting.     

Veterinary medicinal product usage among food animal producers and its health implications in Central Ethiopia

Background

Antimicrobials and anthelmintics are the most commonly used veterinary drugs to control animal diseases. However, widespread use of these drugs could contribute to the emergence of drug resistance. Information on the practice of antimicrobial usage among food animal raising communities in Central Ethiopia is scarce. We used a standardised questionnaire survey to assess knowledge, awareness, and practices related to drug use and resistance in food animals among the farmers in and around Bishoftu town.

Results

Of the total of 220 livestock owners interviewed, around 80% of the respondents were not able to define what antimicrobials are and for what purposes they are used. Only 14.1% (n?=?31) of the respondents had awareness about antimicrobial resistance (AMR) and its consequences; and 35.5% (n?=?11/31) and 9.7% (n?=?3/31) of them agreed that the irrational use of antimicrobials in animals could lead to AMR in animals and humans. Oxytetracycline was the most commonly available antibiotic in veterinary drug shops/pharmacies and the most widely used drug in the area. However, 43.3% of the respondents did not see clinical improvements after using antibiotics. Similarly, the respondents explained that no response was observed in 73.3, 70.8 and 52.5% of the cases after medication with anthelmintics, antiprotozoal and acaricides, respectively. About 56.7% of the respondents considered traditional medicines equally important to modern medicines. It was also noted that there were illegal drug vendors, dispensing medicines under unfavourable conditions which include a direct exposure to sunlight, which practice violates the drug handling and storage recommendations given by WHO.

Conclusion

The study revealed that there is a general lack of awareness among food animal owners about the correct use of antibiotics and anthelmintics. The widespread misuse and improper drug dispensing and handling practices observed in this study can affect the drug quality and can also contribute to the development of drug resistance in central Ethiopia.

     

Using the ratio of means as the effect size measure in combining results of microarray experiments

Background  

Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small.     

No evidence for prolonged excretion of polioviruses in persons with residual paralytic poliomyelitis in Ethiopia, Pakistan and Guatemala.

Persons who have developed acute flaccid paralysis following infection with wild-type polioviruses or vaccine-associated paralytic poliomyelitis usually excrete polioviruses for only a few weeks. However, some patients with paralytic poliomyelitis have had prolonged excretion of polioviruses for periods of up to 10 years after onset of disease. Most prolonged excretors have been identified in industrialized countries. We studied 348 patients 2-28 years old in Ethiopia, Pakistan and Guatemala with residual paralytic poliomyelitis to determine if they had IgA or IgG deficiency or persistent poliomyelitis excretion at least 1 year after onset of disease. None of the 348 affected individuals had IgG deficiency or persistent poliovirus excretion. One child had borderline low serum IgA concentration. Since we did not study children under 2 years of age, persons born with IgG deficiency disorders may have died in developing countries where replacement immunoglobulin therapy is not readily available. Nevertheless, persistent poliovirus excretion among persons 2 years of age and older with residual paralytic poliomyelitis is uncommon in developing countries.