ghanaopendata/ghanaian-research-english huggingface dataset:
Variability of redundant scan coverages along the Z-axis and dose implications for common computed tomography examinations

Background Scan length optimization is a method of optimization which ensures that, imaging is performed to cover just the area of interest without unnecessarily exposing structures that would not add value to answer a given clinical question. Purpose This study assessed the variability and degree of redundant scan coverages along the z-axis of CT examinations of common indications and the associated radiation dose implications in CT facilities in Ghana for optimization measures to be recommended. Methods On reconstructed acquired CT images, the study measured extra distances covered above and below anatomical targets for common indications with calibrated calipers across 25 CT facilities. The National Cancer Institute Dosimetry System for CT (NCICT) (Monte Carlo-based-software) was used to simulate the scanning situations and organ dose implications for scans with and without the inclusion of the redundant scan areas. Results A total of 1,640 patients’ CT data sets were used in this study. The results demonstrated that CT imaging utilized varying scan lengths (16.45±21.0–45.99±4.3 cm), and 70.6% of the scans exceeded their pre-defined anatomic boundaries by a mean range of 2.86±1.07–5.81±1.66 cm, thereby resulting in extra patient radiation dose. Hence, scanning without the redundant coverages could generate a dose length product (DLP) reduction of 17.5%, 18.8%, 15.5% and 9.0% without degrading image quality for brain lesion, lung lesion, pulmonary embolism and abdominopelvic lesion CT imaging, respectively, whilst ensuring organ dose reduction of0.8%–79.1%. Conclusion The study strongly recommends that radiographers should avoid the inclusion of redundant areas in CT examinations to reduce organ doses.

Source: UG
Variability of root traits, seed size and tolerance to low soil phosphorus in common bean (Phaseolus vulgaris L.)

Common bean is an important food and cash crop, but its seed yield productivity is constrained by the soil phosphorus (soil-P) deficiency among other factors. This study was implemented to determine variability of root traits and seed size of 14 bean genotypes, and identify genotypes with tolerance to low soil-P. A pot experiment was laid out in split-plot design with two replicates. Highly significant (P<0.01) mean square differences were observed among the genotypes and the genotype×soil-P interactions for all the root traits and seed size. Genotypes BFS-29, USRM-20 and SEF-15 all of Meso-American origin had the lowest values for seed size reduction rate and low fertility susceptibility index and were, therefore, considered tolerant to low soil-P. Cumulatively PC-1 and PC-2 accounted for about 99% of the total variability and were both highly correlated with Hypocotyl Root Length (HRL). PC-2 was also highly correlated with basal root whorl number, basal root growth angle, basal root length and tap root diameter. Quadrant-3 comprised of genotypes USRM-20, SEF-15, BFS-29 and SAB-560 that were tolerant to low soil-P and were characterized with longer basal roots, large tap root diameter, and high seed size. The tolerant genotypes need to be tested on a large scale, conserved and could be utilized in bean improvement programs for low soil-P tolerance.

Source: UG
Variability of sugars in staple-type sweet potato (Ipomoea batatas) cultivars: The effects of harvest time and storage

Total soluble sugar content and composition was studied by high performance liquid chromatography in four high dry-matter sweet potato cultivars at 3, 4, and 5 months maturity. Total soluble sugar consisted of sucrose, glucose, and fructose, ranging from 4.10-10.82 g/100 g (dry-weight basis). At harvest, there were significant differences in total soluble sugar due to maturity (p < 0.001) and cultivar (p < 0.05). The highest total soluble sugar contents were in 5-month samples at harvest (7.36-10.34 g/100 g) and 4-month samples after short-term storage under tropical ambient conditions (8.66-10.82 g/100 g). Estimated amylase enzyme activity varied significantly with harvest age (p < 0.05). Although reducing sugar contents were low, fructose levels in 5-month samples increased considerably after storage. © 2014 Copyright Taylor and Francis Group, LLC.

Source: UG
Variable clinical expression of homozygous beta thalassaemia in a Ghanaian family.

The Epidemiology Department contributes to the mission of the institute through basic and applied epidemiological research on, but not limited to, malaria and other diseases of public health importance. It is also home to the Social Science Unit of the Institute, including the Health Support Centre for HIV/AIDS and other communicable and noncommunicable health problems.

Source: UG
Variant G57E of Mannose Binding Lectin Associated with Protection against Tuberculosis Caused by Mycobacterium africanum but not by M. tuberculosis

Structural variants of the Mannose Binding Lectin (MBL) cause quantitative and qualitative functional deficiencies, which are associated with various patterns of susceptibility to infectious diseases and other disorders. We determined genetic MBL variants in 2010 Ghanaian patients with pulmonary tuberculosis (TB) and 2346 controls and characterized the mycobacterial isolates of the patients. Assuming a recessive mode of inheritance, we found a protective association between TB and the MBL2 G57E variant (odds ratio 0.60, confidence interval 0.4–0.9, P 0.008) and the corresponding LYQC haplotype (Pcorrected 0.007) which applied, however, only to TB caused by M. africanum but not to TB caused by M. tuberculosis. In vitro, M.africanum isolates bound recombinant human MBL more efficiently than did isolates of M. tuberculosis. We conclude that MBL binding may facilitate the uptake of M. africanum by macrophages, thereby promoting infection and that selection by TB may have favoured the spread of functional MBL deficiencies in regions endemic for M. africanum

Source: UG
Variants of LRP2, Encoding a Multifunctional Cell-Surface Endocytic Receptor, Associated with Hearing Loss and Retinal Dystrophy

Hereditary deafness and retinal dystrophy are each genetically heterogenous and clinically variable. Three small unrelated families segregating the combination of deafness and retinal dystrophy were studied by exome sequencing (ES). The proband of Family 1 was found to be compound heterozygous for NM_004525.3: LRP2: c.5005A > G, p.(Asn1669Asp) and c.149C > G, p.(Thr50Ser). In Family 2, two sisters were found to be compound heterozygous for LRP2 variants, p.(Tyr3933Cys) and an experimentally confirmed c.7715 + 3A > T consensus splice-altering variant. In Family 3, the proband is compound heterozygous for a consensus donor splice site variant LRP2: c.8452_8452 + 1del and p.(Cys3150Tyr). In mouse cochlea, Lrp2 is expressed abundantly in the stria vascularis marginal cells demonstrated by smFISH, single-cell and single-nucleus RNAseq, suggesting that a deficiency of LRP2 may compromise the endocochlear potential, which is required for hearing. LRP2 variants have been associated with Donnai–Barrow syndrome and other multisystem pleiotropic phenotypes different from the phenotypes of the four cases reported herein. Our data expand the phenotypic spectrum associated with pathogenic variants in LRP2 warranting their consideration in individuals with a combination of hereditary hearing loss and retinal dystrophy.

Source: UG
Variation in APOL1 contributes to ancestry-level differences in HDLc-kidney function association

Low levels of high-density cholesterol (HDLc) accompany chronic kidney disease, but the association between HDLc and the estimated glomerular filtration rate (eGFR) in the general population is unclear. We investigated the HDLc-eGFR association in nondiabetic Han Chinese (HC, n = 1100), West Africans (WA, n = 1497), and African Americans (AA, n = 1539). There were significant differences by ancestry: HDLc was positively associated with eGFR in HC (β = 0.13, P 0.0001), but negatively associated among African ancestry populations (WA: -0.19, P 0.0001; AA: -0.09, P = 0.02). These differences were also seen in nationally-representative NHANES data (among European Americans: 0.09, P = 0.005; among African Americans -0.14, P = 0.03). To further explore the findings in African ancestry populations, we investigated the role of an African ancestry-specific nephropathy risk variant, rs73885319, in the gene encoding HDL-associated APOL1. Among AA, an inverse HDLc-eGFR association was observed only with the risk genotype (-0.38 versus 0.001; P = 0.03). This interaction was not seen in WA. In summary, counter to expectation, an inverse HDLc-eGFR association was observed among those of African ancestry. Given the APOL1 × HDLc interaction among AA, genetic factors may contribute to this paradoxical association. Notably, these findings suggest that the unexplained mechanism by which APOL1 affects kidney-disease risk may involve HDLc.

Source: UG
Variation in bioactive phytochemicals and sensory attributes of osmosonic convective dried ginger from four African countries

BACKGROUND: The rhizome of ginger (Zingiber officinale Roscoe) is one of the most patronized spices worldwide and plays an important role in folklore medicine. In this study, we aimed to determine the quality of ginger samples from representative West African (Ghana, Nigeria) and East African (Uganda, Kenya) countries. By that, we also implicitly sought to determine the probable influence of location of cultivation (and the intrinsic growth conditions) on the quality of the samples. The ginger samples were pretreated by osmosonication prior to relative humidity convective drying and analyzed for differences in their metabolomes, total phenolic content (TPC) and total flavonoid content (TFC), antioxidant activities, sensory characteristics and volatile compounds composition (via electronic-nose determination). RESULTS: The outcome of our study showed marked source-dependent differences in the metabolomes of the samples as captured by a metabolomics approach. Based on the findings of the metabolomics study, 6-gingerol content was quantified and found to be higher in the samples of West African origin. Also, the samples from the two West African countries contained higher levels of bioactive phytochemicals as evinced by the results of TPC, TFC, e-nose analysis, and antioxidant activities. They also gave better sensory attributes. CONCLUSION: In summary, for all parameters assessed, and on a country-by-country basis, the general quality trend observed was: Ghana > Nigeria > Uganda > Kenya. All results taken together, our findings at least in part, point to the influence of geographical regions of cultivation on the quality of the ginger rhizomes.

Source: UG
Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities

Previously published data from our group and others demonstrate that human milk oligosaccharide (HMOs), as well as milk and infant fecal microbial profiles, vary by geography. However, little is known about the geographical variation of other milk-borne factors, such as lactose and protein, as well as the associations among these factors and microbial community structures in milk and infant feces. Here, we characterized and contrasted concentrations of milk-borne lactose, protein, and HMOs, and examined their associations with milk and infant fecal microbiomes in samples collected in 11 geographically diverse sites. Although geographical site was strongly associated with milk and infant fecal microbiomes, both sample types assorted into a smaller number of community state types based on shared microbial profiles. Similar to HMOs, concentrations of lactose and protein also varied by geography. Concentrations of HMOs, lactose, and protein were associated with differences in the microbial community structures of milk and infant feces and in the abundance of specific taxa. Taken together, these data suggest that the composition of human milk, even when produced by relatively healthy women, differs based on geographical boundaries and that concentrations of HMOs, lactose, and protein in milk are related to variation in milk and infant fecal microbial communities.

Source: UG
Variation in optineurin (OPTN) allele frequencies between and within populations

Purpose: To evaluate the extent to which mutations in the optineurin (OPTN) glaucoma gene play a role in glaucoma in different populations. Methods: Case-controlled study of OPTN sequence variants in individuals with or without glaucoma in populations of different ancestral origins and evaluate previous OPTN reports. We analyzed 314 subjects with African, Asian, Caucasian and Hispanic ancestries included 229 cases of primary open-angle glaucoma, 51 cases of juvenile-onset open-angle glaucoma, 33 cases of normal tension glaucoma, and 371 controls. Polymerase chain reaction-amplified OPTN coding exons were resequenced and case frequencies were compared to frequencies in controls matched for ancestry. Results: The E50K sequence variant was identified in one individual from Chile with normal tension glaucoma, and the 691_692insAG variant was found in one Ashkenazi Jewish individual from Russia. The R545Q variant was found in two Asian individuals with primary open-angle glaucoma; one of Filipino ancestry and one of Korean ancestry. In addition to presenting OPTN allele frequencies for Caucasian and Asian populations that have been the subject of previous reports, we also present information for populations of Hispanic and black African ancestries. Conclusions: Our study contributes additional evidence to support the previously reported association of the OPTN E50K mutation with glaucoma. After finding an additional 691_692insAG OPTN variant, we can still only conclude that this variant is rare. Combined analysis of our data with data from more than a dozen other studies indicates no association of R545Q with glaucoma in most populations. Those same studies disagree in their conclusions regarding the role of M98K in glaucoma. Our analysis of the combined data provides statistically significant evidence of association of M98K with normal tension glaucoma in Asian populations, but not in Caucasian populations; however, the validity of this conclusion is questionable because of large differences in allele frequencies between and within populations. It is currently not possible to tell how much of the underlying cause of the allele frequency difference is attributable to demographic, technical, or ascertainment differences among the studies. © 2006 Molecular Vision.

Source: UG
Variation in percentage weight bearing with changes in standing posture during water immersion: Implication for clinical practice

Background: The degree of weightlessness during water immersion is usually estimated through percentage weight bearing (PWB). However, variations in PWB in different standing postures have not been documented. The study was designed to investigate the PWB of apparently healthy individuals in four standing postures at the anterior superior iliac spine level of immersion.Methods: One hundred and ninety-three consenting undergraduates were purposively enlisted in this study. Participants' body weight (BW) was measured on land as well as in Erect Standing (ES), Grasp-Inclined-Prone-Standing (GIPS), Half-Grasp-Inclined-Towards-Side Standing (HGITSS) and Inclined-Standing with Head Support (ISHS) postures in hydro pool, using a specially designed water-proof weighing scale. PWB was calculated by dividing BW in water by BW on land and multiplying by 100. Data were analyzed using mean, standard deviation and ANOVA at α=0.05.Results: The mean age and BW (on land) of the participants were 22.4 years and 60.7 kg respectively. Participants' PWB were significantly different (p < 0.05) across the four standing postures. PWB was highest in ES and lowest in ISHS; PWB in ES (52.3 ± 5.8) being significantly higher (p < 0.001) than that observed in the derived standing postures. Further, PWB in GIPS (43.3 ± 5.6) and ISHS (43.2 ± 7.3) were significantly lower than in HGITSS (47.4 ± 5.2) posture while PWB in GIPS and ISHS postures were not significantly different (p > 0.05).Conclusion: Changes in standing posture have significant effect on PWB in hydro pool. The finding has implication for partial weight bearing exercises in hydro pool. © 2014 Adegoke et al.

Source: UG
Variation in percentage weight bearing with changes in standing posture during water immersion: implication for clinical practice

Abstract Background The degree of weightlessness during water immersion is usually estimated through percentage weight bearing (PWB). However, variations in PWB in different standing postures have not been documented. The study was designed to investigate the PWB of apparently healthy individuals in four standing postures at the anterior superior iliac spine level of immersion. Methods One hundred and ninety-three consenting undergraduates were purposively enlisted in this study. Participants&#8217; body weight (BW) was measured on land as well as in Erect Standing (ES), Grasp-Inclined-Prone-Standing (GIPS), Half-Grasp-Inclined-Towards-Side Standing (HGITSS) and Inclined-Standing with Head Support (ISHS) postures in hydro pool, using a specially designed water-proof weighing scale. PWB was calculated by dividing BW in water by BW on land and multiplying by 100. Data were analyzed using mean, standard deviation and ANOVA at &#945;&#8201;=&#8201;0.05. Results The mean age and BW (on land) of the participants were 22.4&#160;years and 60.7&#160;kg respectively. Participants&#8217; PWB were significantly different (p&#8201;&lt;&#8201;0.05) across the four standing postures. PWB was highest in ES and lowest in ISHS; PWB in ES (52.3&#8201;&#177;&#8201;5.8) being significantly higher (p&#8201;&lt;&#8201;0.001) than that observed in the derived standing postures. Further, PWB in GIPS (43.3&#8201;&#177;&#8201;5.6) and ISHS (43.2&#8201;&#177;&#8201;7.3) were significantly lower than in HGITSS (47.4&#8201;&#177;&#8201;5.2) posture while PWB in GIPS and ISHS postures were not significantly different (p&#8201;&gt;&#8201;0.05). Conclusion Changes in standing posture have significant effect on PWB in hydro pool. The finding has implication for partial weight bearing exercises in hydro pool.

Source: UG
Variation in plasma concentrations of insulin-like growth factor-l in pasture-fed Holstein cows

The objective of this 5-wk study was to determine dietary effects on plasma concentrations of insulin-like growth factor-l (IGF-I), as well as milk production and milk components in pasture-fed dairy cows. Thirty-two Holstein cows 4 to 5 wk postpartum were randomly assigned to 4 dietary subgroups. Feed was provided twice daily ad libitum at 0900 and 1600 h composed of fresh-cut pasture, meadow hay, and pelleted cereal grain to achieve differing levels of DMI and ME density (LL: 16.6 kg of DMI and 174 MJ of ME; HL: 17.3 kg of DMI and 181.1 MJ of ME; LH: 15.4 kg of DMI and 183.1 MJ of ME; HH: 17.9 kg of DMI and 213.3 MJ of ME with the first letter indicating DMI and the second ME, and with H indicating high and L indicating low, respectively). The first day cows were placed on their diets was designated d 0. Concentrations of IGF-I were measured in frozen-thawed samples of plasma using a verified ELISA. Dietary treatment had affected plasma concentrations of IGF-I by d 7 with cows on high ME diets having greater IGF-I concentrations at d 14 (83.7 vs. 45.6 ng/mL) than cows on the low ME diets. The level of DMI had less effect on plasma concentrations of IGF-I at d 14 (72.2 vs. 57.1 ng/mL). Dietary treatment effects on these concentrations had stabilized by d 21. Day-to-day variation in mean plasma concentrations of IGF-I within each dietary treatment was low during an intensive period of daily sampling for 14 d (from d 22 to 35). Within-cow day-to-day variation was also low compared with that among cows within the same dietary group and was associated with a high repeatability in the day-to-day concentration of IGF-I in individual cows. Intraclass correlation coefficients for IGF-I ranged from 0.56 (+ 0.14) to 0.88 (± 0.06) with a combined (pooled) value for the 4 subgroups of 0.77 (±0.05). The ME and DMI effects (H vs. L) at d 35 were 79.3 vs. 41.4 and 62.0 vs. 55.7 ng/mL, respectively. Although the ME and DMI differences also affected milk yield and compositional parameters, the effects were not as proportionately great as those measured for IGF-I. Altering the ME or DMI components of the pasture-based diets produced changes in plasma IGF-I concentrations that did not become stabilized for 3 wk, but were then highly repeatablefor individual cows within each dietary group. Both observations have relevance to interpreting data related to plasma concentrations of IGF-I in lactating Holstein cows.

Source: UG
Variation in Plasmodium falciparum erythrocyte invasion phenotypes and merozoite ligand gene expression across different populations in areas of malaria endemicity

Plasmodium falciparum merozoites use diverse alternative erythrocyte receptors for invasion and variably express cognate ligands encoded by the erythrocyte binding antigen (eba) and reticulocyte binding-like homologue (Rh) gene families. Previous analyses conducted on parasites from single populations in areas of endemicity revealed a wide spectrum of invasion phenotypes and expression profiles, although comparisons across studies have been limited by the use of different protocols. For direct comparisons within and among populations, clinical isolates from three different West African sites of endemicity (in Ghana, Guinea, and Senegal) were cryopreserved and cultured ex vivo after thawing in a single laboratory to assay invasion of target erythrocytes pretreated with enzymes affecting receptor subsets. Complete invasion assay data from 67 isolates showed no differences among the populations in the broad range of phenotypes measured by neuraminidase treatment (overall mean, 40.6% inhibition) or trypsin treatment (overall mean, 83.3% inhibition). The effects of chymotrypsin treatment (overall mean, 79.2% inhibition) showed heterogeneity across populations (Kruskall-Wallis P = 0.023), although the full phenotypic range was seen in each. Schizont-stage transcript data for a panel of 8 invasion ligand genes (eba175, eba140, eba181, Rh1, Rh2a, Rh2b, Rh4, and Rh5) were obtained for 37 isolates, showing similar ranges of variation in each population except that eba175 levels tended to be higher in parasites from Ghana than in those from Senegal (whereas levels of eba181 and Rh2b were lower in parasites from Ghana). The broad diversity in invasion phenotypes and gene expression seen within each local population, with minimal differences among them, is consistent with a hypothesis of immune selection maintaining parasite variation. © 2015, American Society for Microbiology.

Source: UG
Variation in rice cadmium related to human exposure

Cereal grains are the dominant source of cadmium in the human diet, with rice being to the fore. Here we explore the effect of geographic, genetic, and processing (milling) factors on rice grain cadmium and rice consumption rates that lead to dietary variance in cadmium intake. From a survey of 12 countries on four continents, cadmium levels in rice grain were the highest in Bangladesh and Sri Lanka, with both these countries also having high per capita rice intakes. For Bangladesh and Sri Lanka, there was high weekly intake of cadmium from rice, leading to intakes deemed unsafe by international and national regulators. While genetic variance, and to a lesser extent milling, provide strategies for reducing cadmium in rice, caution has to be used, as there is environmental regulation as well as genetic regulation of cadmium accumulation within rice grains. For countries that import rice, grain cadmium can be controlled by where that rice is sourced, but for countries with subsistence rice economies that have high levels of cadmium in rice grain, agronomic and breeding strategies are required to lower grain cadmium. © 2013 American Chemical Society.

Source: UG