Measuring the three-dimensional shear from simulation data, with applications to weak gravitational lensing

We have developed a new three-dimensional algorithm, based on the standard P$^3$M method, for computing deflections due to weak gravitational lensing. We compare the results of this method with those of the two-dimensional planar approach, and rigorously outline the conditions under which the two approaches are equivalent. Our new algorithm uses a Fast Fourier Transform convolution method for speed, and has a variable softening feature to provide a realistic interpretation of the large-scale structure in a simulation. The output values of the code are compared with those from the Ewald summation method, which we describe and develop in detail. With an optimal choice of the high frequency filtering in the Fourier convolution, the maximum errors, when using only a single particle, are about 7 per cent, with an rms error less than 2 per cent. For ensembles of particles, used in typical $N$-body simulations, the rms errors are typically 0.3 per cent. We describe how the output from the algorithm can be used to generate distributions of magnification, source ellipticity, shear and convergence for large-scale structure.Comment: 22 pages, latex, 11 figure

The revolving door of mental, neurological, and substance use disorders re-hospitalization in rural KwaZulu-Natal Province, South Africa.

Objective: Little is known about the extent of mental, neurological and substance-use (MNS) disorders re-hospitalization in South Africa. We examined the extent of one-year MNS re-hospitalization (MNS-R) in a rural South African primary health care facility (PHCF). Methods: We conducted a retrospective analysis of hospital administrative data from 10,525 adults discharged from a rural PHCF in KwaZulu-Natal Province, South Africa. Chi-squared tests were utilized to describe MNS-R within one year of an index hospital admission in individuals with MNS, with a sub-analysis also being conducted to describe schizophrenia re-hospitalization (S-R). Results: The prevalence of MNS and schizophrenia recorded at an index hospitalization was 5% and 1%, respectively. A total of 44/67 (66%) individuals with a diagnosis of MNS at the index hospitalization were classified as having MNS-R during oneyear follow-up period. Half of those diagnosed with schizophrenia at the index hospitalization (6/12 patients) were classified as having S-R during one-year follow-up period. There was a significant association between re-hospitalization outcomes (MNS-R and S-R) and MNS (p<0.01) or schizophrenia diagnosis (p<0.01) at index baseline hospitalization. Conclusion: The extent of MNS-R and S-R remains relatively high in rural South Africa, and needs further health systems strengthening to prevent revolving door occurrences

Human gene copy number spectra analysis in congenital heart malformations

The clinical significance of copy number variants (CNVs) in congenital heart disease (CHD) continues to be a challenge. Although CNVs including genes can confer disease risk, relationships between gene dosage and phenotype are still being defined. Our goal was to perform a quantitative analysis of CNVs involving 100 well-defined CHD risk genes identified through previously published human association studies in subjects with anatomically defined cardiac malformations. A novel analytical approach permitting CNV gene frequency “spectra” to be computed over prespecified regions to determine phenotype-gene dosage relationships was employed. CNVs in subjects with CHD (n = 945), subphenotyped into 40 groups and verified in accordance with the European Paediatric Cardiac Code, were compared with two control groups, a disease-free cohort (n = 2,026) and a population with coronary artery disease (n = 880). Gains (≥200 kb) and losses (≥100 kb) were determined over 100 CHD risk genes and compared using a Barnard exact test. Six subphenotypes showed significant enrichment (P ≤ 0.05), including aortic stenosis (valvar), atrioventricular canal (partial), atrioventricular septal defect with tetralogy of Fallot, subaortic stenosis, tetralogy of Fallot, and truncus arteriosus. Furthermore, CNV gene frequency spectra were enriched (P ≤ 0.05) for losses at: FKBP6, ELN, GTF2IRD1, GATA4, CRKL, TBX1, ATRX, GPC3, BCOR, ZIC3, FLNA and MID1; and gains at: PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, HRAS, GATA6 and RUNX1. Of CHD subjects, 14% had causal chromosomal abnormalities, and 4.3% had likely causal (significantly enriched), large, rare CNVs. CNV frequency spectra combined with precision phenotyping may lead to increased molecular understanding of etiologic pathways

Impact of \u3cem\u3eMYH6\u3c/em\u3e Variants in Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is a clinically and anatomically severe form of congenital heart disease (CHD). Although prior studies suggest that HLHS has a complex genetic inheritance, its etiology remains largely unknown. The goal of this study was to characterize a risk gene in HLHS and its effect on HLHS etiology and outcome. We performed next-generation sequencing on a multigenerational family with a high prevalence of CHD/HLHS, identifying a rare variant in the α-myosin heavy chain (MYH6) gene. A case-control study of 190 unrelated HLHS subjects was then performed and compared with the 1000 Genomes Project. Damaging MYH6 variants, including novel, missense, in-frame deletion, premature stop, de novo, and compound heterozygous variants, were significantly enriched in HLHS cases (P \u3c 1 × 10−5). Clinical outcomes analysis showed reduced transplant-free survival in HLHS subjects with damaging MYH6 variants (P \u3c 1 × 10−2). Transcriptome and protein expression analyses with cardiac tissue revealed differential expression of cardiac contractility genes, notably upregulation of the β-myosin heavy chain (MYH7) gene in subjects with MYH6 variants (P \u3c 1 × 10−3). We subsequently used patient-specific induced pluripotent stem cells (iPSCs) to model HLHS in vitro. Early stages of in vitro cardiomyogenesis in iPSCs derived from two unrelated HLHS families mimicked the increased expression of MYH7 observed in vivo (P \u3c 1 × 10−2), while revealing defective cardiomyogenic differentiation. Rare, damaging variants in MYH6 are enriched in HLHS, affect molecular expression of contractility genes, and are predictive of poor outcome. These findings indicate that the etiology of MYH6-associated HLHS can be informed using iPSCs and suggest utility in future clinical applications

Predictors of quality of life among community psychiatric patients in a peri-urban district of Gauteng province, South Africa

Introduction: Few studies on quality of life (QoL) in the mentally ill population of South Africa have been conducted, but none in community-dwelling individuals. This study examined the QoL of psychiatric patients at community mental health clinics in Gauteng province of South Africa. Methods: A cross-sectional interview-based study was conducted on 121 adult patients attending community psychiatric clinics. To reduce the impact of acute psychiatric symptoms on subjective QoL, only clinically stable patients were included. Instruments used included the World Health Organization Quality of Life BREF domains (i.e. physical health, psychological health, social relationships and environment), the Brief Psychiatric Rating Scale (BPRS) for severity of illness and a socio-demographic and clinical questionnaire. Results: Just under half of the sample rated their overall QoL as good or very good. The strongest predictor of a poor QoL in all four domains was residual psychiatric symptomatology. The most severe BPRS scores were for the symptoms of depression, anxiety and somatic concern. Perceived social support significantly predicted a better QoL in the psychological, social relationships and environmental domains. Conclusion: This study highlights the negative impact of residual psychiatric symptoms on subjective QoL, and the importance of social support and enhancing QoL. If better QoL is the goal of care, then our findings highlight the importance of managing residual symptoms and promoting social support

Weak gravitational lensing in the standard Cold Dark Matter model, using an algorithm for three-dimensional shear

We investigate the effects of weak gravitational lensing in the standard Cold Dark Matter cosmology, using an algorithm which evaluates the shear in three dimensions. The algorithm has the advantage of variable softening for the particles, and our method allows the appropriate angular diameter distances to be applied to every evaluation location within each three-dimensional simulation box. We investigate the importance of shear in the distance-redshift relation, and find it to be very small. We also establish clearly defined values for the smoothness parameter in the relation, finding its value to be at least 0.88 at all redshifts in our simulations. From our results, obtained by linking the simulation boxes back to source redshifts of 4, we are able to observe the formation of structure in terms of the computed shear, and also note that the major contributions to the shear come from a very broad range of redshifts. We show the probability distributions for the magnification, source ellipticity and convergence, and also describe the relationships amongst these quantities for a range of source redshifts. We find a broad range of magnifications and ellipticities; for sources at a redshift of 4, 97{1/2}% of all lines of sight show magnifications up to 1.3 and ellipticities up to 0.195. There is clear evidence that the magnification is not linear in the convergence, as might be expected for weak lensing, but contains contributions from higher order terms in both the convergence and the shear.Comment: 14 pages, LaTeX, 15 figures include

Green environment and incident depression in South Africa : a geospatial analysis and mental health implications in a resource-limited setting

Our results imply the importance of green environments for mental wellbeing in sub-Saharan African settings experiencing rapid urbanisation, economic and epidemiological transition, reaffirming the need to incorporate environmental services and benefits for sustainable socioeconomic development.Peer reviewe

Relationship between physical activity and behaviour challenges of adolescents in South Africa.

BACKGROUND: Four out of five adolescents worldwide are physically inactive based on recommended standards. AIM: We determined whether physical activity is associated with lower behavioural challenges in adolescents to promote buy-in from stakeholders. SETTING: KwaZulu-Natal province, South Africa, from January 2020 to March 2020. METHODS: A cross-sectional study was conducted among 187 adolescent learners (12-18 years) from three government schools in KwaZulu-Natal Province, South Africa, from January to March 2020. We fitted linear regression models between the Strengths and Difficulties Questionnaire scores (total, internalising, externalising, and prosocial) and hours of physical activity exposure, adjusting for demographic covariates, and depression history. RESULTS: The median age was 14.4 years (interquartile range = 1.36) and 75.9% of the participants were females. Overall average and weekday physical activity were each associated with lower total and externalising but higher pro-social scores. Depression was associated with higher inactivity scores (total, internalising and externalising). CONCLUSIONS: The article shows that physical activity can reduce the behavioural and emotional problems in adolescents. CONTRIBUTION: Physical activity is critical for a healthy adolescent hood and needs to be actively included in childhood development

Beyond HIV prevalence: identifying people living with HIV within underserved areas in South Africa

Introduction Despite progress towards the Joint United Nations Programme on HIV/AIDS 95-95-95 targets, South Africa is still suffering from one of the largest HIV epidemics globally. In this study, we generated high-resolution HIV prevalence maps and identified people living with HIV (PLHIV) in underserved areas to provide essential information for the optimal allocation of HIV-related services. Methods The data come from the South Africa Demographic and Health Survey conducted in 2016 and spatial variables from other published literature. We produced high-resolution maps of HIV prevalence and underserved areas, defined as a greater than 30 min travel time to the nearest healthcare facility. Using these maps and the population density, we mapped PLHIV and the PLHIV within underserved areas for 30, 60 and 120 min thresholds. Results There was substantial geographic variation in HIV prevalence, ranging from 1.4% to 24.2%, with a median of 11.5% for men, and from 2.1% to 48.1%, with a median of 20.6% for women. Gauteng province showed the highest density for both HIV prevalence and PLHIV. 80% of all areas in the country were identified as underserved areas (30 min threshold), which contained more than 16% and 20% of the total men and women living with HIV, respectively. KwaZulu-Natal province had the largest number of PLHIV in underserved areas (30 min threshold) and showed less than one healthcare facility per 1000 PLHIV. Conclusion Our study showed extensive spatial variation of HIV prevalence and significant numbers of PLHIV in underserved areas in South Africa. Moreover, we identified locations where HIV-related services need to be intensified to reach the ~1.5 million PLHIV in underserved areas, particularly in KwaZulu-Natal province, with less than one healthcare facility per 1000 PLHIV

Sexual trauma and post-traumatic stress among African female refugees and migrants in South Africa

Background: While there is considerable research in developed countries on the nature and extent of post-traumatic stress among refugees and migrants, few report on female Africans migrating within Africa. Aim: The aim of this study was to investigate the association between exposure to traumatic life events and post-traumatic stress disorder risk in refugees and migrants in Durban, South Africa, with specific focus on sexual trauma events among women. Methods: Interviews were conducted on 157 consenting non-South African adults using a sociodemographic questionnaire, Life Events Checklist (documenting traumatic events experienced) and the Harvard Trauma Questionnaire (measuring post-traumatic symptomatology). Associations between total number of traumatic events and post-traumatic stress were explored using adjusted regression models. Results: The results of one model indicated that greater numbers of traumatic life events experienced by women were associated with raised odds of post-traumatic stress disorder risk (β = 1.48; p < 0.001). Another model indicated that exposure to sexual trauma events were associated with greater odds of post-traumatic stress disorder risk (β = 4.09; p = 0.02). Conclusion: Our findings highlight the critical importance of mental health service for females with history of sexual traumatic events for this vulnerable population