ghanaopendata/ghanaian-research-english huggingface dataset:
A Genomic Infection Control Study for Staphylococcus Aureus in two Ghanaian Hospitals

Background: Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. The aim of the study was to apply WGSA to elucidate the possible transmission events involved in two suspected Staphylococcus aureus hospital outbreaks in Ghana and describe genomic features of the S. aureus isolates sampled in the outbreaks. Methods: The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The S. aureus isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the S. aureus isolates was performed and the sequence reads were mapped to the S. aureus reference genome of strain USA300_FPR3757. A maximum-likelihood phylogenetic tree was reconstructed. Multilocus sequence typing together with the analysis of antimicrobial resistance and virulence genes were performed by short read mapping using the SRST2. Results: The S. aureus isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the blaZ gene, with low prevalence of tetK and dfrG genes also observed. All isolates were mecA negative. The pvl genes were common and observed in distinct lineages that revealed diverse Sa2int phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of S. aureus ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred. Conclusion: The pattern of dissemination of the ST15 clone in the emergency ward of Korle- Bu Teaching Hospital highlights a basic problem with disinfection of environmental surfaces at the hospital. Diverse phage population rather than a single highly transmissible phage type likely mediates the high prevalence of pvl genes among the S. aureus isolates.

Source: UCC
Genomic prediction of tropical maize resistance to fall armyworm and weevils: genomic selection should focus on effective training set determination

Genomic selection (GS) can accelerate variety release by shortening variety development phase when factors that influence prediction accuracies (PA) of genomic prediction (GP) models such as training set (TS) size and relationship with the breeding set (BS) are optimized beforehand. In this study, PAs for the resistance to fall armyworm (FAW) and maize weevil (MW) in a diverse tropical maize panel composed of 341 double haploid and inbred lines were estimated. Both phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) were predicted using 17 parametric, semi-parametric, and nonparametric algorithms with a 10-fold and 5 repetitions cross-validation strategy. n. For both MW and FAW resistance datasets with an RBTS of 37%, PAs achieved with BLUPs were at least as twice as higher than those realized with BLUEs. The PAs achieved with BLUPs for MW resistance traits: grain weight loss (GWL), adult progeny emergence (AP), and number of affected kernels (AK) varied from 0.66 to 0.82. The PAs were also high for FAW resistance RBTS datasets, varying from 0.694 to 0.714 (for RBTS of 37%) to 0.843 to 0.844 (for RBTS of 85%). The PAs for FAW resistance with PBTS were generally high varying from 0.83 to 0.86, except for one dataset that had PAs ranging from 0.11 to 0.75. GP models showed generally similar predictive abilities for each trait while the TS designation was determinant. There was a highly positive correlation (R=0.92***) between TS size and PAs for the RBTS approach while, for the PBTS, these parameters were highly negatively correlated (R=-0.44***), indicating the importance of the degree of kinship between the TS and the BS with the smallest TS (31%) achieving the highest PAs (0.86). This study paves the way towards the use of GS for maize resistance to insect pests in sub-Saharan Africa

Source: UCC
Genomics and Epigenomics of Congenital Heart Defects: Expert Review and Lessons Learned in Africa

Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infra- structure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated. We present an expert review on CHD with lessons learned on Africa. We found variable CHD phenotype prevalence in Africa across countries and populations. There are important gaps and paucity in genomic studies of CHD in African populations. Among the available genomic studies, the key findings in Africa were variants in GATA4 (P193H), MTHFR 677TT, and MTHFR 1298CC that were associated with atrial septal defect, ventricular septal defect (VSD), Tetralogy of Fallot (TOF), and patent ductus arteriosus phenotypes and 22q.11 deletion, which is associated with TOF. There were no data on epigenomic association of CHD in Africa, however, other studies have shown an altered expression of miR-421 and miR-1233-3p to be associated with TOF and hypermethylation of CpG islands in the promoter of SCO2 gene also been associated with TOF and VSD in children with non-syndromic CHD. These findings signal the urgent need to develop and implement genetic and genomic research on CHD to identify the hereditary and genome–environment inter- actions contributing to CHD. These projected studies would also offer comparisons on CHD pathophysiology between African and other populations worldwide. Genomic research on CHD in Africa should be developed in parallel with next generation technology policy research and responsible innovation frameworks that examine the social and political factors that shape the emergence and societal embedding of new technologies.

Source: UCC
Genotoxic and Cytotoxic Activity of Aqueous Extracts of Croton membranaceus in Rodent Bone Marrow and Human Benign Prostate Hyperplasic Cells

Background: Croton membranaceus is a plant cherished by traditional healers in Ghana for its anti-prostate cancer properties. Its cytotoxic effect as well as safety has been proved. However, to the best of our knowledge, no study has been conducted to assess its genotoxic and cytotoxic potential using the rodent bone marrow and colony formation assays respectively. Aims: This study is aimed at investigating the cytotoxic and genotoxic effects of the aqueous root extract of Croton membranaceus (CMARE) using the colony formation and rodent bone marrow assays respectively. Study Design: This was an experimental study. Methodology: To determine the cytotoxic effect, BPH-1 cells were seeded in 6-well plates at a density of 1.0 x 105 cells/well in 2 mL culture medium (plus 10% FBS) and incubated for 24 h. After treatment with 0, 1, 3 and 5 mg/ml of CMARE for 48 h, the cells were collected and further treated with fresh medium in the absence of CMARE, and reseeded into new 6-well plates at a density of 1.0 x 103 cells / well. After 10 days incubation, colonies were fixed in 10% formalin, crystal violetstained and counted. Genotoxicity was determined by the bone marrow assay using 30 male Sprague-Dawley rats divided equally into three groups. Animals in the treatment, positive and negative control groups were administered 3000 mg/kg CMARE, N-nitroso-N-methylurea and saline respectively. Results: Cytotoxicity significantly occurred at 3 and 5 mg/ml, compared to the control. The bone marrow assay showed a significant difference between CMARE-treated animals and negative controls when the polychromatic erythrocyte-normochromatic erythrocyte (PCE-NCE) ratios were compared. Furthermore, there was a positive correlation between CMARE-treated animals and positive controls when their micronucleated polychromatic erythrocytes (MNPCE) were compared, indicating similar genotoxic potential between very high CMARE doses and the positive control. Conclusion: These results show that CMARE has both cytotoxic and genotoxic potential.

Source: UCC
Genotypic distribution of human oncogenic papillomaviruses in sexually active women in Burkina Faso: Central, Central-Eastern and HautsBassins regions

Objective: this study was conducted to determine the distribution of high-risk human papillomavirus (HR-HPV) genotypes in women in the general population of three regions of Burkina Faso. METHOD: This multicenter, descriptive cross-sectional study involved 1321 sexually active women in five cities in three regions of Burkina Faso: Central, Central-Eastern and Hauts-Bassins regions. After collection of endocervical specimens, pre-cervical lesions were screened by visual inspection with acetic acid and lugol (VIA / VILI). HR-HPV genotypes were characterized by multiplex real-time PCR after extraction of viral DNA. Results: The mean age of women was 31.98 ± 10.09 years. The HR-HPV infection in the three regions ranged from 26.16% to 43.26% with 35.42% as overall prevalence in women. The most common HR-HPV genotypes in descending order were: HPV 56, 52, 66, 59, 39, 51, 18, 35. The prevalence of bivalent vaccine genotypes (HPV16 / 18) was 7.83% against 63.78% of genotypes not covered by HPV vaccine; 36.32% (170/468) of women had multiple concomitant HR-HPV infections. Conclusion: this study showed significant regional variation and high prevalence of HR-HPV infection in women. The predominant genotypes differ from those covered by available vaccines in Burkina Faso. These results will help guide our health policies towards better prevention of cervical cancer. The diversity of oncogenic genotypes is sparking a large-scale study in the West African sub-region, particularly in cases of cancer and the introduction of the nonavalent vaccine which includes HPV 52 found among the predominant genotypes in this study.

Source: UCC
A genre analysis of news bulletins on selected Ghanaian radio stations

The study aimed to explore how journalists construct news bulletins on Ghanaian radio stations. Specifically, the study sought to examine the generic structures of news bulletins and how journalists draw on other sources for the writing of their texts. Four radio stations (Joy FM, Citi FM, Radio XYZ and Radio Ghana) were selected. The total number of data set comprised 20 transcribed episodes of radio news bulletins from the four radio stations. The analysis of the data set was done by drawing on Halliday and Hasan’s (1985) Generic Structural Potential framework and Bazerman’s (2004) Intertextuality framework. The study revealed three key findings. First, radio news from the four stations analyzed is characterized by twelve rhetorical elements. Second, journalists largely utilize explicit and implicit intertextual sources. Finally, journalists predominantly used positive reporting verbs in their reportage to indicate that they agree and support the information quoted. The findings of this research have significant implication for the genre theory and pedagogy.

Source: UCC
A genre analysis of the introduction sections of sports news presentation on selected Ghanaian television stations

The study aimed to present a genre analysis of the introduction sections of sports news presentation programmes (SNPP) on selected television stations in Ghana. Specifically, the study sought to account for the schematic structure (that is the various rhetorical units, the sequence of moves, the textual space of each move identified) and some lexico-grammatical resources that are dominant in the selected rhetorical unit that was analyzed. Three television stations (GTV, Metro TV & TV3) were selected. The total number of data set comprised 50 transcribed episodes of the SNPP from the three television stations. The analysis of the data set was done by drawing on the perspective of Swales (1990) and Bhatia (1993). Aside this, the study employed the AntConc software to account for some keywords and their collocates as evident in the data set. The findings revealed that the introduction section of the SNPP of the three stations analyzed is characterized by six-move rhetorical structure. With respect to the language use, it was identified that majority of the keywords found in the introduction section consisted of what Scott (1999) calls the ‘aboutness’ variety which include words that tell us about the genre of the corpus. The findings of this research have pedagogical implication as well as having implication for the genre theory.

Source: UCC
Genre analysis of undergraduate dissertation conclusions

Genre analysis has gained so much interest among genre analysts all over the world. Inasmuch as there has been this growing interest in genre analysis, it appears that research into undergraduate writing is still in its infancy. This study investigates the undergraduate writing, specifically dissertations authored by undergraduate students from the lenses of ESP tradition. The data for the study comprises concluding chapters of forty (40) dissertations from two departments—Chemistry and History—in the University of Cape Coast. Using Bunton (2005) as my analytical framework, the study revealed eight moves: Move1 (Stating the aim(s) of the chapter), Move 2 (Restating the objective(s) of the study), Move 3 (Describing the methods used), Move 4 (Summarizing the study), Move 5 (Giving recommendation(s)), Move 6 (Stating challenges), Move 7 (Extending well wishes) and Move 8 (Stating the importance of the study). All the eight moves identified were present in the Department of History Conclusions (DHCs). Out of the eight moves identified, only six were present in the Department of Chemistry Conclusions (DCCs). Pertaining to the lexico-grammatical resources in the various moves, the AntConc software was used to tease out the keywords in the various moves. Collocates of the keywords that were common to moves across the disciplines were also identified. It can be concluded that conclusions from the two selected departments vary in terms of their titles, schematic structure as well as the keywords that typify the moves identified.

Source: UCC
Geographic distribution of global economic important mahogany complex: a review

Mahogany is the collective international trade name for the high-value tropical and subtropical timber tree species of the family Meliaceae. Mahogany species are noted for their deep red-brown heartwood and are widely used in the construction, boat building, interior decoration (particularly paneling and floor tiles), and in the manufacture of furniture. Across their natural geographical distribution range, many rural communities depend for their livelihoods on the genetic resources of the species as they provide natural products and services. However, mahogany populations across their native range are threatened by deforestation, habitat fragmentation, excessive logging and genetic erosion. In addition, climate change may bring about a shift in the distributional range of the native species. To safeguard the rich diversity of mahogany requires a conscientious effort in policy formulation and the enforcement of existing laws in regard to the management and conservation of the species. In addition, it is imperative that mahogany is used as an integral component in agroforestry systems and in reforestation efforts, as well as in the restoration of degraded forest ecosystems in order to protect the genetic resources of the species. The aim of this review was to highlight the threats to the sustainability of the species. We conducted literature review to examine the geographic distributional range of a mahogany complex (Khaya spp, Entandrophragma spp, Cedrela spp, Toona spp, Swietenia spp) at global, regional and ecosystem scales. We used maps as annotated diagrams to show the probable geographic global distribution range of the mahogany complex. The Khaya spp. and Entandrophragma spp. are native to Africa, Cedrela spp. And Swietenia spp. are native to Central and South America, whereas, Toona spp. are found primarily in southeast Asia

Source: UCC
Geographic population structure of the African malaria vector Anopheles gambiae suggests a role for the forest-savannah biome transition as a barrier to gene flow

The primary frotropical malaria mosquito vector Anopheles ambiae sensu stricto has a complex population structure. In West Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviors. To investigate patterns of macro geographic population substructure, 25 An. Ambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M-form being subdivided into distinct west, central, and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast, geographically patterned population substructure appears much weaker within the S-form

Source: UCC
Geographical Distribution of β-Lactam Resistance among Klebsiella spp. from Selected Health Facilities in Ghana

β-Lactam-resistant Klebsiella isolates continue to cause multidrug resistance infections worldwide. This study aimed to describe the geographical distribution of extended spectrum β-lactamase (ESBL), AmpC β-lactamase (AmpC), and carbapenemase production among 139 Klebsiella isolates recovered from patients at major referral health facilities in Ghana. The phenotypic methods of combined disc diffusion test, modified three-dimensional test, modified Hodge test (MHT), and combined disc test were performed for each isolate to detect ESBL, AmpC, carbapenemase, and metallo-β-lactamase (MBL) producers, respectively. Except for MBL, all other β-lactam resistance mechanisms were highest in the healthcare facilities situated in the northern belt of Ghana. Significant regional difference of ESBL producers was observed between the northern and middle belts as well as the northern and southern belts. Genotypic detection with polymerase chain reaction (PCR) revealed the presence of bla TEM 36/139 (25.9%), bla SHV 40/139 (28.8%), bla CTX-M 37/139 (26.6%), bla OXA-48 3/139 (2.16%), and bla NDM 1/139 (0.72%) genotypes. In conclusion, there were variations in β-lactam resistance among Klebsiella spp. from health facilities situated in the northern, middle, and southern belts of Ghana. The study provides preliminary evidence that emphasizes the need to direct more attention to antimicrobial resistance control, especially in the northern belt of Ghana. Findings from this study may e critical for creating and fine-tuning effective antimicrobial resistance Control strategies and for informing accurate antibiotic prescription y practitioners

Source: UCC
Geographical Distribution of β-Lactam Resistance among Klebsiella spp. from Selected Health Facilities in Ghana

β-Lactam-resistant Klebsiella isolates continue to cause multidrug resistance infections worldwide. This study aimed to describe the geographical distribution of extended spectrum β-lactamase (ESBL), AmpC β-lactamase (AmpC), and carbapenemase production among 139 Klebsiella isolates recovered from patients at major referral health facilities in Ghana. The phenotypic methods of combined disc diffusion test, modified three-dimensional test, modified Hodge test (MHT), and combined disc test were performed for each isolate to detect ESBL, AmpC, carbapenemase, and metallo-β-lactamase (MBL) producers, respectively. Except for MBL, all other β-lactam resistance mechanisms were highest in the healthcare facilities situated in the northern belt of Ghana. Significant regional difference of ESBL producers was observed between the northern and middle belts as well as the northern and southern belts. Genotypic detection with polymerase chain reaction (PCR) revealed the presence of bla TEM 36/139 (25.9%), bla SHV 40/139 (28.8%), bla CTX-M 37/139 (26.6%), bla OXA-48 3/139 (2.16%), and bla NDM 1/139 (0.72%) genotypes. In conclusion, there were variations in β-lactam resistance among Klebsiella spp. from health facilities situated in the northern, middle, and southern belts of Ghana. The study provides preliminary evidence that emphasizes the need to direct more attention to antimicrobial resistance control, especially in the northern belt of Ghana. Findings from this study may be critical for creating and fine-tuning effective antimicrobial resistance control strategies and for informing accurate antibiotic prescription by practitioners.

Source: UCC
The Geography Teacher as an Effective Classroom Manager

The Geography Teacher in the classroom setting is confronted on a daily basis with situations which require effective decision-making. By and large, the quality of the decision s/he makes daily determines the attainment of her/his instructional goals. But unfortunately, some teachers are unable to attain their instructional goals due to their poor decision-making skills. This article is an attempt to educate teachers in general and geography teachers in particular on the decision-making skills that they have to demonstrate in the teaching learning process. The article deals with issues such as the functional roles of the Geography Teacher as regards lesson planning, lesson implementation and lesson evaluation. In performing these functions, the Geography Teacher will have to demonstrate her/his decision-making skills with regard to what to teach, when to teach, how to teach and how to evaluate.

Source: UCC
Geohydrological Characteristics of Landfills to Groundwater Sensitivity: A Case of Oti Landfill Site, Kumasi.

Soil plays a crucial role in preservation of groundwater resources from contamination and pollution. In view of this, the study focused on the geophysical and chemical condition of the Oti landfill soil and also assessed the physicochemical characteristics of local groundwater and leachate. The groundwater quality assessment tool was used to assess the impact of the Oti landfill site on the local groundwater. Systematic, grab and quartering sampling techniques were used to sample the soil, leachate and groundwater. On the leachate and groundwater samples, in-situ measurements were made to record the pH, EC and TDS concentration. Three different pits with depth 150 cm each were dug at the landfill site and three different samples were taken from each pit at varying depths. Samples were taken to the laboratory under a temperature below 4OC. Parameters that were analysed included K+, Ca2+, Mg2+, Na+, Al3+, BOD, COD, DO and some selected heavy metals including Fe3+, Zn, Cu, Mn, As, Cd, and Pb. Results obtained from the groundwater samples showed that the water was still in a good condition for usage. Hydrogeophysical data of the study area was also collected and the DRASTIC model was used to generate a DRASTIC vulnerability index in assessing how vulnerable the local groundwater was to pollution and also to validate the laboratory results. Both the vulnerability and sensitivity analysis results validated the laboratory results showing that the landfill has had no negative effect on the local groundwater system.

Source: UCC