The General Primordial Cosmic Perturbation

We consider the most general primordial cosmological perturbation in a universe filled with photons, baryons, neutrinos, and a hypothetical cold dark matter (CDM) component within the framework of linearized perturbation theory. We give a careful discussion of the different allowed modes, distinguishing modes which are regular at early times, singular at early times, or pure gauge. As well as the familiar growing and decaying adiabatic modes and the baryonic and CDM isocurvature modes we identify two {\it neutrino isocurvature} modes which do not seem to have been discussed before. In the first, the ratio of neutrinos to photons varies spatially but the net density perturbation vanishes. In the second the photon-baryon plasma and the neutrino fluid have a spatially varying relative bulk velocity, balanced so that the net momentum density vanishes. Possible mechanisms which could generate the two neutrino isocurvature modes are discussed. If one allows the most general regular primordial perturbation, all quadratic correlators of observables such as the microwave background anisotropy and matter perturbations are completely determined by a $5\times 5,$ real, symmetric matrix-valued function of co-moving wavenumber. In a companion paper we examine prospects for detecting or constraining the amplitudes of the most general allowed regular perturbations using present and future CMB data.Comment: 18 pages, 2 Postscript figures, uses revtex. Revised 2-2000 Minor errors corrected and some references adde

Constraining Isocurvature Perturbations with CMB Polarization

The role of cosmic microwave background (CMB) polarisation data in constraining the presence of primordial isocurvature modes is examined. While the MAP satellite mission will be unable to simultaneously constrain isocurvature modes and cosmological parameters, the PLANCK mission will be able to set strong limits on the presence of isocurvature modes if it makes a precise measurement of the CMB polarisation sky. We find that if we allow for the possible presence of isocurvature modes, the recently obtained BOOMERANG measurement of the curvature of the universe fails. However, a comparably sensitive polarisation measurement on the same angular scales will permit a determination of the curvature of the universe without the prior assumption of adiabaticity.Comment: 4pages, Latex with four eps figures. (Revised 18 Dec 2000. Minor typos corrected

Rules of engagement: perspectives on stakeholder engagement for genomic biobanking research in South Africa

Background: Genomic biobanking research is undergoing exponential growth in Africa raising a host of legal, ethical and social issues. Given the scientific complexity associated with genomics, there is a growing recognition globally of the importance of science translation and community engagement (CE) for this type of research, as it creates the potential to build relationships, increase trust, improve consent processes and empower local communities. Despite this level of recognition, there is a lack of empirical evidence of the practise and processes for effective CE in genomic biobanking in Africa. Methods: To begin to address this vacuum, 17 in-depth face to face interviews were conducted with South African experts in genomic biobanking research and CE to provide insight into the process, benefits and challenges of CE in South Africa. Emerging themes were analysed using a contextualised thematic approach. Results: Several themes emerged concerning the conduct of CE in genomic biobanking research in Africa. Although the literature tends to focus on the local community in CE, respondents in this study described three different layers of stakeholder engagement: community level, peer level and high level. Community level engagement includes potential participants, community advisory boards (CAB) and field workers; peer level engagement includes researchers, biobankers and scientists, while high level engagement includes government officials, funders and policy makers. Although education of each stakeholder layer is important, education of the community layer can be most challenging, due to the complexity of the research and educational levels of stakeholders in this layer. Conclusion: CE is time-consuming and often requires an interdisciplinary research team approach. However careful planning of the engagement strategy, including an understanding of the differing layers of stakeholder engagement, and the specific educational needs at each layer, can help in the development of a relationship based on trust between the research team and various stakeholder groups. Since the community layer often comprises vulnerable populations in low and middle income countries (LMICs), co-development of innovative educational tools on genomic biobanking is essential. CE is clearly a component of a broader process best described as stakeholder engagement

MeerKAT's View of the Bullet Cluster 1E 0657-55.8

The Bullet cluster (1E 0657-55.8) is a massive merging system at redshift $z$=0.296, known to host a powerful radio halo and a relic. Here we present high fidelity MeerKAT L-band (0.9-1.7 GHz) observations of the Bullet cluster, in which we trace a larger extent of both the radio halo and relic in comparison to previous studies. The size of the recovered radio halo is 1.6 Mpc $\times$ 1.3 Mpc and the largest linear size of the relic is ~988 kpc. We detect a new decrement feature on the southern outskirts of the halo emission, where a region appears to have a lower surface brightness in comparison to its surroundings. The fainter extension on the outskirts of the radio halo suggests a new wave of merger activity. An in-band spectral index map of the radio halo reveals a hint of radial steepening towards the edges of the diffuse source, likely due to synchrotron electron ageing. The integrated spectral index of the radio halo is 1.1$\pm$0.2. We perform a radio-X-ray surface brightness point-to-point analysis, which reveals a linear correlation for the radio halo. This indicates that the radio halo emission is produced by primary re-acceleration mechanisms. Finally, we derive a radio Mach number of M_R= 4.6$\pm$0.9 for the relic shock region, which is higher than the Mach number inferred by earlier analyses based on X-ray data. Discrepancies between radio and X-ray Mach numbers have been observed for multiple systems, with studies suggesting that this is due to various factors, including relic orientation.Comment: 11 pages, 6 figures. Submitted to MNRAS; corrected typo in the Mach numbe

Consent for critical care research after death from COVID-19: Arguments for a waiver

Pandemics challenge clinicians and scientists in many ways, especially when the virus is novel and disease expression becomes variable or unpredictable. Under such circumstances, research becomes critical to inform clinical care and protect future patients. Given that severely ill patients admitted to intensive care units are at high risk of mortality, establishing the cause of death at a histopathological level could prove invaluable in contributing to the understanding of COVID-19. Postmortem examination including autopsies would be optimal. However, in the context of high contagion and limited personal protective equipment, full autopsies are not being conducted in South Africa (SA). A compromise would require tissue biopsies and samples to be taken immediately after death to obtain diagnostic information, which could potentially guide care of future patients, or generate hypotheses for finding needed solutions. In the absence of an advance written directive (including a will or medical record) providing consent for postmortem research, proxy consent is the next best option. However, obtaining consent from distraught family members, under circumstances of legally mandated lockdown when strict infection control measures limit visitors in hospitals, is challenging. Their extreme vulnerability and emotional distress make full understanding of the rationale and consent process difficult either before or upon death of a family member. While it is morally distressing to convey a message of death telephonically, it is inhumane to request consent for urgent research in the same conversation. Careful balancing of the principles of autonomy, non-maleficence and justice becomes an ethical imperative. Under such circumstances, a waiver of consent, preferably followed by deferred proxy consent, granted by a research ethics committee in keeping with national ethics guidance and legislation, would fulfil the basic premise of care and research: first do no harm. This article examines the SA research ethics framework, guidance and legislation to justify support for a waiver of consent followed by deferred proxy consent, when possible, in urgent research after death to inform current and future care to contain the pandemic in the public interest

Comorbidity in context: Part 1. Medical considerations around HIV and tuberculosis during the COVID-19 pandemic in South Africa

Infectious diseases pandemics have devastating health, social and economic consequences, especially in developing countries such as South Africa. Scarce medical resources must often be rationed effectively to contain the disease outbreak. In the case of COVID-19, even the best-resourced countries will have inadequate intensive care facilities for the large number of patients needing admission and ventilation. The scarcity of medical resources creates the need for national governments to establish admission criteria that are evidence-based and fair. Questions have been raised whether infection with HIV or tuberculosis (TB) may amplify the risk of adverse COVID-19 outcomes and therefore whether these conditions should be factored in when deciding on the rationing of intensive care facilities. In light of these questions, clinical evidence regarding inclusion of these infections as comorbidities relevant to intensive care unit admission triage criteria is investigated in the first of a two-part series of articles. There is currently no evidence to indicate that HIV or TB infection on their own predispose to an increased risk of infection with SARS-CoV-2 or worse outcomes for COVID-19. It is recommended that, as for other medical conditions, validated scoring systems for poor prognostic factors should be applied. A subsequent article examines the ethicolegal implications of limiting intensive care access of persons living with HIV or TB

Comorbidity in context: Part 2. Ethicolegal considerations around HIV and tuberculosis during the COVID-19 pandemic in South Africa

The COVID-19 pandemic has brought discussions around the appropriate and fair rationing of scare resources to the forefront. This is of special importance in a country such as South Africa (SA), where scarce resources interface with high levels of need. A large proportion of the SA population has risk factors associated with worse COVID-19 outcomes. Many people are also potentially medically and socially vulnerable secondary to the high levels of infection with HIV and tuberculosis (TB) in the country. This is the second of two articles. The first examined the clinical evidence regarding the inclusion of HIV and TB as comorbidities relevant to intensive care unit (ICU) admission triage criteria. Given the fact that patients with HIV or TB may potentially be excluded from admission to an ICU on the basis of an assumption of lack of clinical suitability for critical care, in this article we explore the ethicolegal implications of limiting ICU access of persons living with HIV or TB. We argue that all allocation and rationing decisions must be in terms of SA law, which prohibits unfair discrimination. In addition, ethical decision-making demands accurate and evidence-based strategies for the fair distribution of limited resources. Rationing decisions and processes should be fair and based on visible and consistent criteria that can be subjected to objective scrutiny, with the ultimate aim of ensuring accountability, equity and fairness

The initial conditions of the universe: how much isocurvature is allowed?

We investigate the constraints imposed by the current data on correlated mixtures of adiabatic and non-adiabatic primordial perturbations. We discover subtle flat directions in parameter space that tolerate large (~60%) contributions of non-adiabatic fluctuations. In particular, larger values of the baryon density and a spectral tilt are allowed. The cancellations in the degenerate directions are explored and the role of priors elucidated.Comment: 4 pages, 4 figures. Submitted to PR