ghanaopendata/ghanaian-research-english huggingface dataset:
High serum prostate-specific antigen levels in the absence of prostate cancer in Middle-Eastern men: The clinician's dilemma

OBJECTIVE: To investigate the common causes of total serum prostate-specific antigen (PSA) values of > 10 ng/mL in an Arab population, as in the LISA and Europe the risk of prostate cancer is considered high in men with such PSA levels. PATIENTS AND METHODS: Serum total PSA was measured in men presenting to our hospital as part of the investigation for prostate cancer screening and/or in elderly men with prostatism. Men with a serum PSA level of > 10 ng/mL were further investigated by transrectal ultrasonography (TRUS) of the prostate and biopsy of suspicious lesions for histological diagnosis. In addition, the percentage of free PSA, PSA velocity and PSA density were determined. All the patients included in this study were men of Arab origin residing in Kuwait. RESULTS: In all, 1700 men (mean age 55.6 years, range 35-94) were assessed; of these, 161 had a serum PSA of > 10 ng/mL, attributable to benign prostatic hyperplasia (BPH) in 110 (68%), BPH with histological features of prostatitis in 33 (21%) and prostate cancer in 18 (11%). TRUS of the prostate in 143 of the 161 men with either BPH or BPH with prostatitis showed varying grades of intraprostatic calcifications in 22 (15%). Both PSA density and percentage free PSA did not contribute to determining the causes of total PSA levels of > 10 ng/mL. There was a progressive decline in PSA in all patients with BPH and prostatitis, except one who at rebiopsy had prostate cancer (T1NOMO, G1). CONCLUSION: Total PSA values of > 10 ng/mL in Arab men may be a result of BPH, BPH with prostatitis or prostate cancer, in that order. A gradual decline in total PSA (decreased PSA velocity) with time to < 4 ng/mL often confirms the diagnosis of BPH with prostatitis. The percentage of free PSA and PSA density may not be helpful in diagnosing prostate cancer with certainty in these patients. Compared with Caucasians in the USA and Europe, BPH and BPH with prostatitis appear to be more frequent causes of serum PSA levels of > 10 ng/mL in Arab men.

Source: UG
High Soil Phosphorus Application Significantly Increased Grain Yield, Phosphorus Content but Not Zinc Content of Cowpea Grains

To ameliorate the impact of soil phosphorus (P) deficiency on cowpea, the use of P-based fertilizers is recommended. Plant zinc (Zn) is an essential nutrient required by plants in a wide range of processes, such as growth hormone production and metabolism. However, a negative association between plant Zn content and high P application has been reported in some crops. There are few reports about soil P application and plant Zn content relationship on cowpea. Thus, this study investigated the response of cowpeas to three P rates in the screenhouse (0, 1.5, and 30 mg P/kg) and field (0, 10, and 60 kg P2O5/ha) and their effects on plant P and Zn content, biomass, and grain yield. In the screenhouse, shoot and root dry weights, and shoot P and Zn content were measured. Shoot dry weight, grain yield, grain P, and Zn contents were determined from field plants. Higher rates of P led to increased shoot biomass and grain yield of the field experiment but were not associated with a significant change in shoot or grain Zn content. There was not a significant correlation between grain yield and Zn content in high soil P (p < 0.05). The effect of higher P application on reduced plant Zn contents may be genotype-dependent and could be circumvented if genotypes with high Zn content under high soil P are identified.

Source: UG
High uptake of Intermittent Preventive Treatment of malaria in pregnancy is associated with improved birth weight among pregnant women in Ghana

Despite the clinically proven advantages of intermittent preventive treatment of malaria in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), utilisation has been low in many African countries. To increase uptake and achieve the desired effect, the World Health Organization revised the policy to a monthly administration. Assessing the coverage and impact of the revised policy on pregnancy and neonatal outcomes is, therefore, a necessity. A 2-parallel cross-sectional hospital-based study was carried out among pregnant women attending first antenatal care (ANC) and delivery. Maternal and cord blood samples were assayed for malaria parasites by quantitative PCR targeting both the 18S rDNA and the acidic terminal segment of Plasmodium falciparum var genes, and plasma SP levels were measured by liquid chromatography coupled to tandem mass spectrometry. Parasite prevalence was similar between the two study sites but decreased significantly between the first ANC (9% or 43%) and delivery (4% or 11%) based on the qPCR target. At delivery, 64.5% of women received ≥3 IPTp-SP dose, 15.5% received 2 doses and 6% had 1 dose. Taking ≥3 IPTp-SP doses was associated with an average birth weight increase of more than 0.165 kg. IPTp-SP uptake was associated with plasma SP level at delivery (OR = 32.3, p ≤ 0.005, 95% CI (13.3;78.4) for those that reported ≥3 IPTp-SP doses) while the same trend of improved birth weight was observed with high plasma SP levels. The new IPTp policy is well implemented and well utilised by women in the sites considered in this study and translates to the improved birth weight observed. This study confirms the interest and the clinical benefit expected from this policy change.

Source: UG
A High-Density Admixture Map for Disease Gene Discovery in African Americans

Admixture mapping (also known as “mapping by admixture linkage disequilibrium,” or MALD) provides a wayof localizing genes that cause disease, in admixed ethnic groups such as African Americans, with∼100 times fewermarkers than are required for whole-genome haplotype scans. However, it has not been possible to perform powerfulscans with admixture mapping because the method requires a dense map of validated markers known to have largefrequency differences between Europeans and Africans. To create such a map, we screened through databasescontaining∼450,000 single-nucleotide polymorphisms (SNPs) for which frequencies had been estimated in Africanand European population samples. We experimentally confirmed the frequencies of the most promising SNPs in amultiethnic panel of unrelated samples and identified 3,011 as a MALD map (1.2 cM average spacing). We estimatethat this map is∼70% informative in differentiating African versus European origins of chromosomal segments.This map provides a practical and powerful tool, which is freely available without restriction, for screening fordisease genes in African American patient cohorts. The map is especially appropriate for those diseases that differin incidence between the parental African and European populations.

Source: UG
High‑density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

Introduction Common bean is one of the widely consumed food security crop in Africa, Asia, and South America. Under standing genetic diversity and population structure is crucial for designing breeding strategies. Materials Two hundred and eighty-nine germplasm were recently collected from diferent regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers. Results The overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces col lected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classifcation. Model-based structure analysis delineated the 289 com mon bean genotypes into six hypothetical ancestoral populations. Conclusions The genotypes were not clustered based on geographical regions and they were not the main drivers for the diferentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing efective collection and conservation for efcient utilization for the improve ment of the cro

Source: UG
High-level cerebellar expression of cytokines and adhesion molecules in fatal, paediatric, cerebral malaria

Although the roles played by systemic tumour necrosis factor (TNF) and interleukin 1beta (IL-1beta), and their upregulation of intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1) and E-selectin, in the pathogenesis of human cerebral malaria (CM) are well established, the role of local cytokine release, in the brain, remains unclear. Immunohistochemistry was therefore used to compare the expression of ICAM-1, VCAM-1, E-selectin, IL-1beta, TNF and transforming growth factor beta (TGF-beta) at light-microscope level, in cryostat sections of cerebral, cerebellar and brainstem tissues collected, post-mortem, from Ghanaian children. Among the 21 children investigated were 10 cases of CM, five of severe malarial anemia (SMA), one of purulent bacterial meningitis (PBM), two of non-central-nervous-system infection (NCNSI) and three children who had no infection (NI) when they died. Parasitised erythrocytes were detected in all of the sections from the cases of fatal malaria (CM and SMA), and sequestered leucocytes were present in most of the sections from the CM cases (but none of the sections from the SMA cases). Significantly elevated vascular expression of all three adhesion molecules investigated was detected in the brains of the 15 cases of fatal malaria and one of the cases of NCNSI (a child with Salmonella septicaemia), and in the malaria cases this showed highly significant co-localization with the areas of erythrocyte sequestration. In terms of the levels of expression of ICAM-1, VCAM-1 and E-selectin, there were, however, negligible differences between the CM and SMA cases. Although TGF-beta showed intravascular and perivascular distribution in all the subjects, its expression was most intense in the PBM case and the CM group. Only in the sections from the PBM and CM cases did TNF and IL-1beta show prominent brain parenchymal staining, in addition to the intravascular and perivascular staining seen in all subjects. The highest observed expression of each of the six antigens studied was in the cerebellar sections of the malaria cases. Endothelial activation in the brain therefore appears to be a feature of fatal malaria and Salmonella sepsis, and in cases of fatal malaria is closely associated with leucocyte sequestration. In the present study, IL-1beta and TNF were only up-regulated in the brains of children with neurodegenerative lesions, whereas TGF-beta was present in all cases.

Source: UG
High-performance liquid chromatographic assay for the simultaneous determination of sulfadoxine and pyrimethamine from whole blood dried onto filter paper.

A method using solid-phase extraction and high-performance liquid chromatography is evaluated for the simultaneous determination of sulfadoxine and pyrimethamine from 0.1 ml of whole blood dried onto filter paper. Extraction recoveries are about 60% for both drugs. The coefficient of variation for intra-assay precision, inter-assay precision and accuracy is less than 10% for sulfadoxine (10-100 microg/ml) and pyrimethamine (1-10 microg/ml).

Source: UG
High-temperature chromium isotope fractionation and its implications: Constraints from the Kızıldağ ophiolite, SE Turkey

Chromium isotope data were obtained from olivine, orthopyroxene and chromite separates of the Kızıldağ ophiolite, SE Turkey, to investigate the effects of high temperature magma processes on Cr isotope fractionation. Harzburgite in the Kızıldağ ophiolite has the δ53Cr values of −0.14 to −0.12‰ in chromite, and −0.08 to −0.01‰ in bulk rocks. These Cr isotope fractionations could be driven by partial melting and metasomatism. The dunite and chromitite samples from the mantle-crust transition zone of the Kızıldağ ophiolite are cumulates, and their chromite and olivine have δ53Cr values of −0.29 to −0.06‰ and −0.11 to 0.41‰, respectively. The δ53Cr values of chromite are negatively correlated with the chemical indices of fractional crystallization (e.g., Fe# of chromite), suggesting that Cr isotopes were fractionated during fractional crystallization. In the chromitite, the degree of Cr isotope fractionation increases with fractional crystallization, with 0.23‰ Cr isotope fractionation occurring at mineral scale. During fractional crystallization, solid phases preferentially incorporate Cr, particularly heavy Cr isotopes, driving the depletion of Cr and enrichment of light Cr isotopes in the evolved melts. The δ53Cr values of olivine are higher than the coexisting chromite, which could be explained by the fact that the olivine grains were probably formed earlier than the chromite. The Cr isotopic features of chromite in the podiform chromitite (−0.22 to −0.04‰) from the mantle sequence are consistent with the modelled fractional crystallization trend, confirming the magmatic origin of the podiform chromitite. Therefore, a significant Cr isotope fractionation at chromite from the Kızıldağ ophiolite could be induced by the high-temperature fractional crystallization. © 2019 Elsevier B.V.

Source: UG
High-throughput analysis of antimalarial susceptibility data by the worldwide antimalarial resistance network (WWARN) In Vitro analysis and reporting tool

Assessment of in vitro susceptibility is a fundamental component of antimalarial surveillance studies, but wide variations in the measurement of parasite growth and the calculation of inhibitory constants make comparisons of data from different laboratories difficult. Here we describe a Web-based, high-throughput in vitro analysis and reporting tool (IVART) generating inhibitory constants for large data sets. Fourteen primary data sets examining laboratory-determined susceptibility to artemisinin derivatives and artemisinin combination therapy partner drugs were collated from 11 laboratories. Drug concentrations associated with half-maximal inhibition of growth (IC 50s) were determined by a modified sigmoid Emax model-fitting algorithm, allowing standardized analysis of 7,350 concentration-inhibition assays involving 1,592 isolates. Examination of concentration-inhibition data revealed evidence of apparent paradoxical growth at high concentrations of nonartemisinin drugs, supporting amendment of the method for calculating the maximal drug effect in each assay. Criteria for defining more-reliable IC50s based on estimated confidence intervals and growth ratios improved correlation coefficients for the drug pairs mefloquine-quinine and chloroquine-desethylamodiaquine in 9 of 11 and 8 of 8 data sets, respectively. Further analysis showed that maximal drug inhibition was higher for artemisinins than for other drugs, particularly in ELISA (enzyme-linked immunosorbent assay)-based assays, a finding consistent with the earlier onset of action of these drugs in the parasite life cycle. This is the first high-throughput analytical approach to apply consistent constraints and reliability criteria to large, diverse antimalarial susceptibility data sets. The data also illustrate the distinct biological properties of artemisinins and underline the need to apply more sensitive approaches to assessing in vitro susceptibility to these drugs. Copyright © 2013, American Society for Microbiology.

Source: UG
High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies

Glycophorins are the most abundant sialoglycoproteins on the surface of human erythro cyte membranes. Genetic variation in glycophorin region of human chromosome 4 (con taining GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodium sp., Babesia sp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for val idation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.

Source: UG
High-throughput tri-colour flow cytometry technique to assess Plasmodium falciparum parasitaemia in bioassays

Abstract Background Unbiased flow cytometry-based methods have become the technique of choice in many laboratories for high-throughput, accurate assessments of malaria parasites in bioassays. A method to quantify live parasites based on mitotracker red CMXRos was recently described but consistent distinction of early ring stages of Plasmodium falciparum from uninfected red blood cells (uRBC) remains a challenge. Methods Here, a high-throughput, three-parameter (tri-colour) flow cytometry technique based on mitotracker red dye, the nucleic acid dye coriphosphine O (CPO) and the leucocyte marker CD45 for enumerating live parasites in bioassays was developed. The technique was applied to estimate the specific growth inhibition index (SGI) in the antibody-dependent cellular inhibition (ADCI) assay and compared to parasite quantification by microscopy and mitotracker red staining. The Bland-Altman analysis was used to compare biases between SGI estimated by the tri-colour staining technique, mitotracker red and by microscopy. Results CPO allowed a better separation between early rings and uRBCs compared to mitotracker red resulting in a more accurate estimate of total parasitaemia. The tri-colour technique is rapid, cost effective and robust with comparable sensitivity to microscopy and capable of discriminating between live and dead and/or compromised parasites. Staining for CD45 improved parasitaemia estimates in ADCI assay since high numbers of leucocytes interfered with the accurate identification of parasitized RBC. The least bias (-1.60) in SGI was observed between the tri-colour and microscopy. Conclusion An improved methodology for high-throughput assessment of P. falciparum parasitaemia under culture conditions that could be useful in different bioassays, including ADCI and growth inhibition assays has been developed.

Source: UG
High-Throughput tri-colour flow cytometry technique to assess Plasmodium falciparum parasitaemia in bioassays

The Department of Immunology conducts research in the field of immunology of infectious and non-infectious diseases. The Department has the overall goal of contributing knowledge to better diagnosis, management, control and prevention of infectious and non-infectious diseases in Ghana and worldwide. This is consistent with the overall strategy of the Noguchi Memorial Institute for Medical Research (NMIMR) and in line with the strategy of the College of Health Sciences of the University of Ghana.

Source: UG
Higher prevalence of antibodies to human herpesvirus 8 in HIV-infected individuals than in the general population in Ghana west Africa

Most research activities involve the use of molecular methods such as regular PCR (PCR), quantitative PCR (Q-PCR), genomic sequence and analysis using different software, genetic engineering, probe hybridization techniques, biological and molecular cloning, evaluation of immune markers for laboratory diagnosis of infections, serological assays involving the use of rapid tests, ELISA-based evaluations and immunofluorescent assay techniques.

Source: UG
Higher production of peripheral blood macrophage migration inhibitory factor in healthy children with a history of mild malaria relative to children with a history of severe malaria

Plasmodium falciparum malaria is one of the leading causes of childhood morbidity and mortality in sub-Saharan Africa. The host immune response to P. falciparum is a critical determinant of malarial pathogenesis and disease outcomes. Macrophage migration inhibitory factor (MIF) is a central regulator of innate immune responses to bacterial and parasitic infections. Our recent investigations demonstrated that peripheral blood MIF production was suppressed in children with severe malaria. Because examination of MIF production in children with active disease does not account for the inherent ability of the host to generate MIF, basal circulating MIF and peripheral blood mononuclear cell (PBMC) MIF transcript levels were determined in healthy children with a history of either mild or severe malaria. Children with prior mild malaria had higher plasma MIF levels and PBMC MIF transcripts than children with an identical number of previous episodes of severe malaria. These results suggest that increased basal MIF production may be important in generating immune responses that protect against the development of severe malaria.

Source: UG
Highly active antiretroviral therapy adherence among perinatally infected HIV adolescents at a teaching hospital in Ghana

Increased accessibility to Antiretroviral Therapy (ART) has resulted in the decline of deaths among children with Perinatally Infected Human Immunodeficiency Virus (PIHIV). Their adherence to Highly Active ART (HAART) is vital for their survival and quality of life. This study aimed at determining HAART medication adherence among adolescents with PIHIV. The study was cross-sectional conducted from September 2015 to January 2016 at a teaching hospital in Ghana. It involved 106 adolescents aged 10-20 years. Morisky's eight-item medication adherence scale was adapted and used to determine the adherence level. Factors influencing adherence were also determined by interviewing the adolescents. EpiData 3.1 and Stata version 12 were used for data entry and analysis respectively. There was low adherence in 76.4% of the adolescents, and the HAART regimen associated with high medication adherence was tenofovir, lamivudine and efavirenz combinations (p = .011). Forgetfulness (p = .001) and inability to come for refill (p = .013) were the main factors associated with low adherence. However adherence was not significantly associated with a lack of medication supply or stigmatization. Addressing the modifiable factors found in this study to be associated with low adherence are essential interventions for their long-term quality of life.

Source: UG