Search

Background: As a result of the COVID-19 pandemic, various clinical intervention methods and AI methods have been employed in the detection, diagnosis, and prognosis of COVID-19 cases. However, limited instances of applying AI to the prognosis of COVID-19 cases in Africa have been reported in the literature. Thus, case studies on the application of machine learning to guide for decision-making on the treatment of COVID-19 cases in Africa are essential. Methods: We applied three machine learning (ML) algorithms: Deep Multi-layer Perceptron (Deep MLP), Extreme Boosted Trees (XGBoost) and Support Vector Machines (SVM) for predicting the outcome of intensive care patients of COVID-19 with comorbidities in a South African hospital. We compared the performance and interpretability of the three ML models when cross-validation (CV) and principal component analysis (PCA) were applied for the prognosis of COVID-19 mortality risk. Results: We found that Deep MLP had the best overall performance when CV and SMOTE were applied without PCA (F1=0.92; AUC = 0.94), followed by SVM (F1=0.83; AUC=0.82). We found that the performance of both SVM and MLP can be enhanced through CV without PCA. XGBoost (F1= 0.81; AUC = 0.79) performed best when none of CV, PCA or SMOTE was applied. XGBoost is not affected by CV and performs worse with PCA. From the model predictions, we identified Length of stay in the hospital, Duration in ICU, Time to ICU from Admission, Days discharged or death, D-dimer (blood clotting factor), and blood pH as the six most critical variables for the prediction of mortality or survival of the COVID-19 patients. We also found other variables: Age at admission, Pf Ratio (PaO2/FiO2 ratio), TropT, Ferritin, ventilation, CRP, and Symptom of Acute respiratory distress syndrome (ARDS) associated with the severity and fatality of COVID-19 cases. Conclusions: This study demonstrates how ML can be applied to identify variables that have prognostic value in the treatment and management of critically ill COVID-19 patients. The findings also reveal the effect of CV and PCA when predicting clinical outcomes of COVID-19 cases

The occurrence of entomopathogenic nematodes (EPNs) in arable soil samples from Nigeria was investigated using Baermann extraction tray and insect-bait (White’s trap) techniques. Isolates were tested for infectivity using the larvae of Galleria mellonella (greater moth) and Tenebrio molitor (mealworm). The study revealed a new species of Heterorhabditis (MT371593) in soil samples that were randomly collected from an arable farmland cultivated with cassava TMS-30572 at the Teaching and Research Farm of Landmark University, Nigeria. Amplification of the internal transcribed spacer region (ITS) of the ribosomal DNA produced a nucleotide sequence of 933 base pairs (bp). A BLASTN search of GenBank showed that the sequence of the Nigerian isolate is identical at 99% similarity to that of Heterorhabditis sp. from Thailand. Infectivity test of the isolate showed 100% mortality against T. molitor larvae within 48 h of exposure while only 80% mortality was recorded for G. mellonella after 1 week of exposure. This is the first account of Heterorhabditis sp. in Nigeria. The varying degrees of infectivity against mealworm and greater moth observed in this study proved that the Nigerian isolate of Heterorhabditis sp. could potentially be an attractive option in the management of insect pests of cash crops.

Summary Root-knot nematodes in the genus Meloidogyne are an important group of plant-parasitic nematodes causing severe damage on agricultural crops worldwide. A study was conducted to identify the species of root-knot nematodes causing damage on honeybush monocultures and to assess the seasonal variations in the nematode population. Soil samples were collected from six experimental sites in Genadendal, Western Cape province of South Africa from 2016 to 2017. DNA was extracted from single-second stage juveniles and species identifi cation was done using species-specifi c sequence-characterised amplifi ed regions (SCAR) primers. Meloidogyne hapla and M. javanica were identifi ed from the sites. Mean population density of the nematodes varied significantly (p < 0.05) in the six sites, with the peak population being recorded in summer of 2017. The study suggests that seasonal variation in temperature and moisture could contribute to changes in the population density of root-knot nematodes in the soil.

Pratylenchus bolivianus (Nematoda, Pratylenchidae) an important parasitic lesion nematode of ornamental and crop plants was found in association with rooibos (Aspalathus linearis) tea in the Cederberg region of South Africa. The population distribution and frequency of occurrence of P. bolivianus on the rooibos orchards were determined, and nematode characterization was done using a combination of traditional morphological characteristics, scanning electron microscopy (SEM), morphometrics and molecular marker by amplifying the D2-D3 expansion segment of the 28S ribosomal RNA gene. P. bolivianus occurred at 84.6% frequency in the sampled fields, with a mean population density that ranged between 10 and 770 lesion nematodes per 250 ml. The morphological features are similar to previous reports, with a slight variation in stylet length and ratio of ‘a’ due to intraspecific geographical variations. The en face view of the SEM shows pattern of the oral disc and first labial annule that is characteristic of P. bolivianus a pattern that falls under Group 2 classification. The phylogenetic relationships as inferred from Maximum Likelihood and Maximum Parsimony revealed a close relationship between the South African isolate of P. bolivianus and those published from other geographical locations. The study confirmed a morphological and genetic similarity between the amphimictic population of P. bolivianus from South Africa and those reported from Costa Rica.

Plant-parasitic nematodes of the genus Xiphinema Cobb, 1913 comprise a complex group of nematode species, some of which are important vectors of plant viruses. During a field survey to determine the soil health of an abandoned honeybush (Cyclopia genistoides) monoculture, a high density of the dagger nematode, Xiphinema oxycaudatum Lamberti & Bleve-Zacheo, 1979 (Nematoda, Dorylaimidae), was observed in soil around the roots of honeybush plants in an abandoned farmland at Bereaville, an old mission station in the Western Cape province of South Africa. Soil samples were taken from the rhizosphere of plants and nematodes were extracted from the soil using a modified extraction tray method. Specimen of the dagger nematodes were processed for scanning electron microscopy, morphological and molecular analysis. Molecular profiling of the nematode species was done in order to give an accurate diagnosis and to effectively discriminate the nematode from other species within the Xiphinema americanum group. Phylogenetic analysis based on the D2D3 expansion segment of the 28S gene supported a close relationship of species within the americanum group, however, the protein-coding cytochrome oxidase (coxI) of the mitochondrial gene provided a useful tool for distinguishing the nematode from other species within the group. This study represents the first report of X. oxycaudatum from South Africa.

Nematodes are important soil organisms that constitute a key component of the soil ecosystem. A plant-parasitic survey was conducted to identify the diversity of nematodes associated with two endemic tea plants, honeybush (Cyclopia spp.) and rooibos (Aspalathus linearis) in the Western Cape province of South Africa. A total of 20 farmlands were surveyed and soil samples were collected from the rhizosphere of plants, for nematode isolation and identification based on morphological characters. Confirmation of the species of plant-parasitic nematodes was done using molecular-based tools. Nematodes were classified into various feeding groups based on their colonizer-persister (c-p) values. Plant-feeding nematodes identified from the honeybush tea plants include; Criconema mutabile, Meloidogyne hapla, M. javanica, and Xiphinema oxycaudatum, while Hoplolaimus sp., Neodolichorhynchus estherae and Pratylechus bolivianus were pathogenic on the rooibos monocultures. Bacterial and fungal feeders (Cephalobidae and Rhabditidae) were also abundant and frequently encountered in all samples. The study provides information on the diversity of nematodes associated with the indigenous herbal tea plants of South Africa., Colonizers; Maturity indices; Morphological identification; Molecular identification; Soil ecosystem.

The genus Helicotylenchus contains cosmopolitan, ubiquitous plant-parasitic nematodes with some species capable of causing significant economic damage to agricultural crops. Accurate species identification in this genus is essential in recognizing the damaging species and establishing effective management options. In a study on cocoa plantations in Nigeria, two species of spiral nematodes were found in high numbers from soil samples obtained from a six-decade old cocoa plantation at the Cocoa Research Institute of Nigeria. An integrated approach involving a combination of morphology, morphometrics, and molecular tools was used to identify the nematode species. Morphological data indicate the presence of both H. multicinctus and H. dihystera. There is congruence in the morphological and molecular data obtained for H. multicinctus. However, phylogenetic analysis of the 28S rDNA expansion segment revealed a high variability in the sequences of the Nigerian population of H. dihystera, suggesting the need for a careful appraisal and more comparative studies.

The genus Vigna (L.) Walp is a large cosmopolitan leguminous genus comprising both cultivated and wild species. Vigna unguiculata (L.) Walp. (Cowpea) is an important food legume that is widely cultivated in the tropics, but its production and storage are hampered by insect pests. The present study evaluated the intra-and inter-specific morphological variabilities among 20 accessions of six Vigna species, comprising wild and cultivated species. The species are Vigna unguiculata (L.) Walp, V. vexillata (A. Richard), V. oblongifolia (A. Richard), V. ambacensis (Baker), V. luteola (Jacq.) (Bentham) and V. racemosa (G. Don) (Hutch and Dalziel). Thirty-one morphological characters involving qualitative and quantitative vegetative and reproductive traits were used for the evaluation. Multivariate analysis such as Pearson Correlation Coefficient (PCC), Principal Component Analysis (PCA) and Cluster Analysis (CA) were employed to evaluate the intra and inter specific variabilities. The paired-sample T test indicated significant differences among the 20 accessions (p#0.000, df = 19) in their morphometric traits. The relative significant correlation observed among some traits such as pod length, number of locules per pod and number of seeds per pod indicated their closeness and potential for genetic improvement of cowpea. The PCA showed that reproductive traits such as days to 50% flowering (0.984), days to 50% ripe pod (0.993), number of pods per peduncle (0.340) and 100-seed weight (0.132) are the major traits that accounted for the variations among the species. The UPGMA using the average (between groups) segregated the 20 accessions into two main clusters, cluster I (comprising mainly wild Vigna species) and cluster II (comprising both wild and cultivated species). The taxonomic affinities and genetic diversity among the species are of great importance in the utilization of the species for food and nutrition, fodder for ruminant animals, cover crop for rotational farming and more importantly genetic improvement of cowpea.

Vegetable crops are highly susceptible to a wide range of pests and diseases among which are the root-knot nematodes (Meloidogyne species). Traditionally, identification of Meloidogyne species had been based on use of morphological characters such as the perennial pattern. In recent times, accuracy of nematode identification using only morphological tools has been challenged due to similarities in morphological characters of some nematode species. The aim of this study was to identify the root-knot nematodes associated with some vegetable crops cultivated on Covenant University farm, Ota, South-west, Nigeria using molecular tools and to determine the population densities of Meloidogyne spp. on the selected vegetable crops. Plant-parasitic nematodes were extracted from soil and roots of Abelmoschus esculentus, Celosia argentea and Core horus olitorius cultivated on Covenant University farm. The nematode species were identified and counted under a compound microscope. The molecular characterization of the Meloidogyne species was done using single adult female nematodes and eggs which were picked out for DNA extraction and amplified with specie-specific primers through Polymerase Chain Reaction (PCR) and separated on 0.5% agarose gel. High population of plant- parasitic nematodes was recorded on the vegetable crops cultivated on covenant university farm. Also significantly higher population (p

Nematode pests of pineapple have not been widely studied in Nigeria compared to other countries. This study investigated the geographical distribution of nematodes associated with pineapple in three pineapple-producing states in Nigeria. A total of 78 farms were sampled from Oyo, Ogun and Osun States using the Agricultural Development Project in each state as a pilot to locate representative farmlands in the States. The modified Baermann Extraction Tray method of Whitehead and Hemming was used for the extraction of vermiform nematodes from soil. Eighteen species of plant-parasitic nematodes (PPN) were found associated with pineapple from the fields surveyed as follows: Meloidogyne incognita, Rotylenchulus reniformis, Pratylenchus brachyurus, Tylenchus sp., Helicotylenchus dihystera, Scutellonema brachyurum, Hoplolaimus pararobustus, Criconemoides limitaneum, Paratylenchus minutus, Gracilaria sp., Hemicriconemoides sp., Hemicycliophora sp., Aphelenchus sp., Aphelenchoides sp., Tylenchorhynchus sp., Paratrophurus sp., Dolichoderus sp. and Xiphinema nigeriense. The most prominent plant-parasitic nematodes found in association with pineapple on all the fields were P. brachyurus, H. dihystera, S. brachyurum, R. reniformis and M. incognita occurring at frequency ratings of 88, 80, 71, 56 and 44%, respectively. The study indicated a widespread distribution of plant-parasitic nematodes of pineapple in Southwestern Nigeria.

This study examines the enterprise combination in cassava based food crop farming system in Ogun state. Three stage sampling technique was used to select 120 cassava farmers from the study area. The data were analyzed using descriptive statistics, economic land equivalent ratio (ELER), linear programming and stochastic production frontier to actualize all the objectives. Descriptive statistics was employed for the description of socio-economic characteristics while economic land equivalent ratio (ELER) and linear programming were used for cost-return structure and optimal combination of crops in cassava based farm enterprises respectively. Descriptive statistics shows that most of the farmers are in their late forty with the mean age of the farmers being 48.2 years with 6years of formal education and wealth of farming experience of about 19 years. The farmers cultivated area of land that varies between 0.5ha and 5 hectare with a mean of 2 hectare. All enterprise combinations are profitable; however, cassava/maize/vegetable production enterprise is the most profitable with net farm income of N36649.90 per hectare closely followed by cassava /maize with N36462.67 per hectare. The optimal cassava based combination was actualized by linear programming model which shows that cassava/maize and cassava/maize/vegetable are the optimal combination because only the two combinations contributed to the gross margin and also added zero opportunity cost to the total cost of production. The result also shows that land and capital are the limiting resources whereas labour is not which means that for optimal cassava based production land and capital investment should be increased. In lieu of these findings, farmers in Ogun state farmers should intercrop cassava, maize and vegetables or intercrop cassava and maize, this will not only increase their net farm income per hectare, it will also ensure flow of income during on and off seasons. Farmers should also increase the utilization of the limiting resources, that is capital base and hectrage of land cultivated. Keywords: Enterprise, Cassava, Farming System, Optimality, Profitability, Intercrop, Linear Programming