The draft genome sequence of Hymenobacter sp. CRA2 isolated from Nama Karoo shrub land soils from South Africa

Here we report the draft genome sequence of Hymenobacter sp. CRA2 isolated from the Nama Karoo shrub land soils of the Northern Cape, South Africa. This genome is approximately 5.88 Mb long and the assembly comprised 45 contigs.http://www.elsevier.com/locate/gdataam2017GeneticsMicrobiology and Plant Patholog

Nonlinear optical properties of metal free and nickel binuclear phthalocyanines

This work employs the open and closed Z-scan aperture technique to comparatively study the nonlinear optical (NLO) properties of nickel and metal free 4-tert-butylphenoxy phthalocyanine, biphenyl bridged bis-4-tert-butylphenoxy phthalocyanine and naphthalene bridged bis-4-tert-butylphenoxy phthalocyanine. Density functional theory (DFT) calculations of dipolar and octupolar ( J=1 and J=3) contribution were determined theoretically from hyper-Rayleigh scattering (HRS) response ( HRS) values

Prevalence and risk factors for Betaherpesvirus DNAemia in children >3 weeks and <2 years of age admitted to a large referral hospital in sub-Saharan Africa

Background. Betaherpesviruses are established causes of morbidity and mortality in immunosuppressed patient groups but have been little studied in sub-Saharan Africa, the epicenter of the human immunodeficiency virus (HIV) pandemic. In this region, primary infections with human cytomegalovirus (HCMV) and human herpesvirus type 6 (HHV-6) type 6 are endemic in infancy, but the clinical impact of these infections among pediatric inpatient groups is poorly characterized and assumptive, based largely on data from Western populations. Methods. We used TaqMan polymerase chain reaction to screen sera from a group of 303 pediatric inpatients aged between 3 weeks and 2 years, at the University Teaching Hospital in Lusaka, Zambia. We report the prevalence of DNAemia and viral loads within this patient group, and evaluate possible clinical associations/risk factors for betaherpesvirus infections in these hospitalized children. Results. We detected betaherpesvirus DNAemia in 59.1% (179/303) of children. HCMV was the most prevalent (41.3%), followed by HHV-6B (20.5%), HHV-7 (20.1%), and HHV-6A (0.3%). HIV infection (odds ratio OR], 2.31; 95% confidence interval CI], 1.37-3.90; P = .002), being underweight (OR, 1.82; 95% CI, 1.06-3.12; P = .03), and an admission diagnosis of suspected meningitis (OR, 5.72; 95% CI, 1.07-30.5; P = .041) were independently associated with an increased odds of HCMV DNAemia. Conversely, HHV-6B and HHV-7 DNAemia were not associated with HIV, underweight, or admission diagnosis. Median HCMV viral load was moderately but significantly higher in HIV-infected children. Conclusions. Highly prevalent HCMV DNAemia was independently associated with HIV infection and being underweight across all age groups, and was also associated with meningitis, with previously underappreciated implications for the health and development of African children

Psychosocial issues and coping mechanisms of pregnant and postnatal women diagnosed with COVID-19: A qualitative study

Objective There is a paucity of data on the psychosocial issues and coping mechanisms among pregnant and postnatal women with COVID-19 infection. We, therefore, aimed to explore the psychosocial issues and coping mechanisms of pregnant and postnatal women diagnosed with COVID-19 at tertiary-level hospitals. Methods This was a qualitative phenomenological study conducted in 2021 with a sample size of 16 women admitted at two referral hospitals serving as COVID-19 admission facilities for pregnant and postnatal women in Lusaka, Zambia. In-depth interviews were conducted via telephone to understand what these women experienced when diagnosed with COVID-19. All the interviews were audio-recorded and transcribed verbatim. Thematic analysis was conducted using the six steps approach to develop emerging themes. Results Two major themes emerged: psychosocial issues and coping mechanisms. The primary psychosocial issues were worry and stigma. Women worried about infecting their unborn baby or neonate, being separated from the baby, the general safety of the baby, and the health of other family members. Women also worried about the attitude of health care providers and faced discrimination or stigma because of their infection. Thus, some coping mechanisms were developed that helped them, such as a positive attitude, keeping the disease secret, reliance on family members for support and using positive information from social media. Conclusion This study provides unique insights into the psychosocial experiences of pregnant and postnatal women diagnosed with COVID-19. Women were particularly concerned about the unborn baby's well-being and discrimination.This study suggests the need for policy and clinical practice to consider the integration of effective mental health services into the provision of maternal health and COVID-19 services

Tuberculosis at post-mortem in inpatient adults at a tertiary referral centre in sub-Saharan Africa - A prospective descriptive autopsy study

Background: The World Health Organisation (WHO) estimates that 3 million cases of tuberculosis (TB) are missed every year. Identification and treatment of these are critical to achieving global TB control. Patients with sub-clinical TB, extra-pulmonary TB, and drug-resistant TB are difficult to diagnose and may be missed at all points of healthcare. An autopsy study was conducted to ascertain the burden of TB at post-mortem in adults who died in the inpatient general medical wards at a tertiary care referral center in Lusaka, Zambia. Methods: Complete whole body autopsies were performed on 125 adult inpatients. Pathological examination involved two stages: (1) Gross pathology was recorded, and samples were taken from all organs for histopathology and cryopreservation; and (2) Histopathological examination of tissue after appropriate staining. Specific pathology and diseases identified on examination were recorded. Lung tissues were processed using the GeneXpert MTB/RIF Assay. Primary outcome measures were specific diseases stratified by HIV status. Secondary outcomes were missed TB and drug-resistant TB cases. Findings: Of 125 adults, median age 35. years (IQR: 29-43), 80 (64%) were male and 101 (80.8%) were HIV-positive. Tuberculosis was the most common finding at autopsy with 78/125 cases (62.4%), of which 66/78 (84.6%) were HIV-infected. There were 35/78 cases (44.9%) with extra-pulmonary TB, the odds of which were higher among HIV-infected cases (aOR 5.14 (95% CI: 1.04-25.4), p=. 0.045); 25.6% (20/78) of the TB cases were not diagnosed ante-mortem; and 13/78 (16.7%) of the TB cases had undiagnosed MDR-TB. Other autopsy findings included: pyogenic pneumonia 36.8% (46/125); bacterial meningitis 7.2% (9/125); cardiac failure 7.2% (9/125); and malignancies 8.8% (11/125). Prevalence of HIV did not differ between TB and non-TB cases (84.6% vs. 74.5%: p=. 0.163). Interpretation: TB remains an important cause of death in adult inpatients. A substantial number of inpatients with TB and MDR-TB are not diagnosed by the current cascade of healthcare. Inpatient settings in high TB endemic countries should be included in WHO 'high risk' groups, and heightened clinical awareness and more proactive screening for TB and MDR-TB in all inpatients should be required

Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry.

Importance:Primary open-angle glaucoma presents with increased prevalence and a higher degree of clinical severity in populations of African ancestry compared with European or Asian ancestry. Despite this, individuals of African ancestry remain understudied in genomic research for blinding disorders. Objectives:To perform a genome-wide association study (GWAS) of African ancestry populations and evaluate potential mechanisms of pathogenesis for loci associated with primary open-angle glaucoma. Design, Settings, and Participants:A 2-stage GWAS with a discovery data set of 2320 individuals with primary open-angle glaucoma and 2121 control individuals without primary open-angle glaucoma. The validation stage included an additional 6937 affected individuals and 14 917 unaffected individuals using multicenter clinic- and population-based participant recruitment approaches. Study participants were recruited from Ghana, Nigeria, South Africa, the United States, Tanzania, Britain, Cameroon, Saudi Arabia, Brazil, the Democratic Republic of the Congo, Morocco, Peru, and Mali from 2003 to 2018. Individuals with primary open-angle glaucoma had open iridocorneal angles and displayed glaucomatous optic neuropathy with visual field defects. Elevated intraocular pressure was not included in the case definition. Control individuals had no elevated intraocular pressure and no signs of glaucoma. Exposures:Genetic variants associated with primary open-angle glaucoma. Main Outcomes and Measures:Presence of primary open-angle glaucoma. Genome-wide significance was defined as P &lt; 5 × 10-8 in the discovery stage and in the meta-analysis of combined discovery and validation data. Results:A total of 2320 individuals with primary open-angle glaucoma (mean [interquartile range] age, 64.6 [56-74] years; 1055 [45.5%] women) and 2121 individuals without primary open-angle glaucoma (mean [interquartile range] age, 63.4 [55-71] years; 1025 [48.3%] women) were included in the discovery GWAS. The GWAS discovery meta-analysis demonstrated association of variants at amyloid-β A4 precursor protein-binding family B member 2 (APBB2; chromosome 4, rs59892895T&gt;C) with primary open-angle glaucoma (odds ratio [OR], 1.32 [95% CI, 1.20-1.46]; P = 2 × 10-8). The association was validated in an analysis of an additional 6937 affected individuals and 14 917 unaffected individuals (OR, 1.15 [95% CI, 1.09-1.21]; P &lt; .001). Each copy of the rs59892895*C risk allele was associated with increased risk of primary open-angle glaucoma when all data were included in a meta-analysis (OR, 1.19 [95% CI, 1.14-1.25]; P = 4 × 10-13). The rs59892895*C risk allele was present at appreciable frequency only in African ancestry populations. In contrast, the rs59892895*C risk allele had a frequency of less than 0.1% in individuals of European or Asian ancestry. Conclusions and Relevance:In this genome-wide association study, variants at the APBB2 locus demonstrated differential association with primary open-angle glaucoma by ancestry. If validated in additional populations this finding may have implications for risk assessment and therapeutic strategies

Whole Genome Expression Analysis of Trembling Aspen (\u3ci\u3ePopulus tremuloides\u3c/i\u3e) Genotypes Exposed to Increasing Concentrations of Nickel

Excess metals in the soil are a known type of abiotic stress and many plant species have evolved specific metal resistance mechanisms to cope and avoid or reduce toxicity symptoms. Studies on P. tremuloides genetic response to nickel are limited. This present study aims to 1) Assess gene expression dynamics in P. tremuloides seedlings treated with varying concentrations of nickel salts and, 2) Compare gene expression profiles among the different treatment groups. Trembling aspen (Populus tremuloides) seedlings were treated with varying concentrations of nickel nitrates (150mg Ni / 1 kg of dry soil, 800mg / kg, and 1, 600mg / kg). The whole genome expression was analyzed using Illumina sequencing. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. In general, there was an increase in number of differentially expressed genes as the nickel concentration increased when compared to water. The number of downregulated (439-600) and upregulated (123-560) genes increases with the nickel concentration increase. A detailed analysis suggested that the 800mg / kg nickel concentration is the threshold at which an early abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two calcium binding proteins when compared to water. For the highest nickel concentration, 7-deoxyloganetin glucosyltransferase was highly upregulated while an auxin response factor, Flavonol 3-sulfotransferase, and a predicted ABC transporter family protein were downregulated. The heatmap showed that the genes were grouped into six clusters based on the changes in expression as nickel concentration increased. The cluster of genes that had increased gene expression with increasing nickel concentration also had multiple enriched Gene ontology (GO) terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal activity. GO terms that decreased in expression with increasing nickel concentrations include ATP and ADP binding, protein kinase activity, integral component of membrane, protein phosphorylation and transmembrane transport

Prediction of non-Newtonian head losses through diaphragm valves at different opening positions

Recent work on fully opened rubber-lined diaphragm valves showed that due to the lack of geometric similarity, dynamic similarity could not be established. The laminar flow loss coefficient constant therefore becomes diameter dependent as is the case of turbulent flow loss coefficients. The purpose of this work was to establish if this is the case for all types of diaphragm valves, by testing diaphragm valves from a different manufacturer. Accurate loss coefficient data is critical for energy efficient hydraulic design. Saunders type straight-through diaphragm valves ranging from 40. mm to 100. mm were tested in the fully open, 75%, 50% and 25% open positions, using a range of Newtonian and non-Newtonian fluids. It was found that the laminar flow loss coefficient constant suggested by Hooper (1981) is sufficient for all valve diameters at Reynolds numbers below 10. However, for transitional and turbulent flow the same loss coefficients cannot be applied for more accurate designs for diaphragm valves from different manufacturers.A new correlation has therefore been developed to predict the loss coefficients for straight-through Saunders diaphragm valves at various openings from laminar to turbulent flow regimes

Determinants of Adoption of Minimum Tillage by Cotton Farmers in Eastern Zambia

Conservation agriculture (CA) is heralded as a means to increase yields and reverse land degradation in Sub-Saharan Africa. Low adoption levels have led to a polarized debate about the merits of conservation agriculture with critics questioning the suitability of the technology and proponents calling for increased and better promotion. Combining quantitative and qualitative analysis, this study examines the determinants of adoption of hand-hoe and oxen-draw minimum tillage in Eastern Zambia and the motivations for farmers’ decisions to implement or reject the technologies