SARS-CoV and SARS-CoV-2 display limited neuronal infection and lack the ability to transmit within synaptically connected axons in stem cell-derived human neurons.

Sarbecoviruses such as SARS and SARS-CoV-2 have been responsible for two major outbreaks in humans, the latter resulting in a global pandemic. While sarbecoviruses primarily cause an acute respiratory infection, they have been shown to infect the nervous system. However, mechanisms of sarbecovirus neuroinvasion and neuropathogenesis remain unclear. In this study, we examined the infectivity and trans-synaptic transmission potential of the sarbecoviruses SARS and SARS-CoV-2 in human stem cell-derived neural model systems. We demonstrated limited ability of sarbecoviruses to infect and replicate in human stem cell-derived neurons. Furthermore, we demonstrated an inability of sarbecoviruses to transmit between synaptically connected human stem cell-derived neurons. Finally, we determined an absence of SARS-CoV-2 infection in olfactory neurons in experimentally infected ferrets. Collectively, this study indicates that sarbecoviruses exhibit low potential to infect human stem cell-derived neurons, lack an ability to infect ferret olfactory neurons, and lack an inbuilt molecular mechanism to utilise retrograde axonal trafficking and trans-synaptic transmission to spread within the human nervous system.

An ethics of anthropology-informed community engagement with COVID-19 clinical trials in Africa.

The COVID-19 pandemic has reinforced the critical role of ethics and community engagement in designing and conducting clinical research during infectious disease outbreaks where no vaccine or treatment already exists. In reviewing current practices across Africa, we distinguish between three distinct roles for community engagement in clinical research that are often conflated: 1) the importance of community engagement for identifying and honouring cultural sensitivities; 2) the importance of recognising the socio-political context in which the research is proposed; and 3) the importance of understanding what is in the interest of communities recruited to research according to their own views and values. By making these distinctions, we show that current practice of clinical research could draw on anthropology in ways which are sometimes unnecessary to solicit local cultural values, overlook the importance of socio-political contexts and wider societal structures within which it works, potentially serving to reinforce unjust political or social regimes, and threaten to cast doubt on the trustworthiness of the research. We argue that more discerning anthropological engagement as well as wider collaboration with other social scientists and those working in the humanities is urgently needed to improve the ethics of current biomedical and pharmaceutical research practice in Africa.

Recognising values and engaging communities across cultures: towards developing a cultural protocol for researchers.

Efforts to build research capacity and capability in low and middle income countries (LMIC) has progressed over the last three decades, yet it confronts many challenges including issues with communicating or even negotiating across different cultures. Implementing global research requires a broader understanding of community engagement and participatory research approaches. There is a considerable amount of guidance available on community engagement in clinical trials, especially for studies for HIV/AIDS, even culturally specific codes for recruiting vulnerable populations such as the San or Maori people. However, the same cannot be said for implementing research in global health. In an effort to build on this work, the Pakistan Institute of Living and Learning and University College London in the UK sought to better understand differences in beliefs, values and norms of local communities in Pakistan. In particular, they have sought to help researchers from high income countries (HIC) understand how their values are perceived and understood by the local indigenous researchers in Pakistan. To achieve this end, a group discussion was organised with indigenous researchers at Pakistan Institute of Living and Learning. The discussion will ultimately help inform the development of a cultural protocol for researchers from HIC engaging with communities in LMIC. This discussion revealed five common themes; (1) religious principles and rules, (2) differing concepts of and moral emphasis on autonomy and privacy, (3) importance of respect and trust; (4) cultural differences (etiquette); (5) custom and tradition (gift giving and hospitality). Based on the above themes, we present a preliminary cultural analysis to raise awareness and to prepare researchers from HIC conducting cross cultural research in Pakistan. This is likely to be particularly relevant in collectivistic cultures where social interconnectedness, family and community is valued above individual autonomy and the self is not considered central to moral thinking. In certain cultures, HIC ideas of individual autonomy, the notion of informed consent may be regarded as a collective family decision. In addition, there may still be acceptance of traditional professional roles such as 'doctor knows best', while respect and privacy may have very different meanings.

A Radical Approach to Ebola: Saving Humans and Other Animals.

As the usual regulatory framework did not fit well during the last Ebola outbreak, innovative thinking still needed. In the absence of an outbreak, randomised controlled trials of clinical efficacy in humans cannot be done, while during an outbreak such trials will continue to face significant practical, philosophical, and ethical challenges. This article argues that researchers should also test the safety and effectiveness of novel vaccines in wild apes by employing a pluralistic approach to evidence. There are three reasons to test vaccines in wild populations of apes: i) protect apes; ii) reduce Ebola transmission from wild animals to humans; and iii) accelerate vaccine development and licensing for humans. Data obtained from studies of vaccines among wild apes and chimpanzees may even be considered sufficient for licensing new vaccines for humans. This strategy will serve to benefit both wild apes and humans.

Is magnetic topology important for heating the solar atmosphere?

Magnetic fields permeate the entire solar atmosphere weaving an extremely complex pattern on both local and global scales. In order to understand the nature of this tangled web of magnetic fields, its magnetic skeleton, which forms the boundaries between topologically distinct flux domains, may be determined. The magnetic skeleton consists of null points, separatrix surfaces, spines and separators. The skeleton is often used to clearly visualize key elements of the magnetic configuration, but parts of the skeleton are also locations where currents and waves may collect and dissipate. In this review, the nature of the magnetic skeleton on both global and local scales, over solar cycle time scales, is explained. The behaviour of wave pulses in the vicinity of both nulls and separators is discussed and so too is the formation of current layers and reconnection at the same features. Each of these processes leads to heating of the solar atmosphere, but collectively do they provide enough heat, spread over a wide enough area, to explain the energy losses throughout the solar atmosphere? Here, we consider this question for the three different solar regions: active regions, open-field regions and the quiet Sun. We find that the heating of active regions and open-field regions is highly unlikely to be due to reconnection or wave dissipation at topological features, but it is possible that these may play a role in the heating of the quiet Sun. In active regions, the absence of a complex topology may play an important role in allowing large energies to build up and then, subsequently, be explosively released in the form of a solar flare. Additionally, knowledge of the intricate boundaries of open-field regions (which the magnetic skeleton provides) could be very important in determining the main acceleration mechanism(s) of the solar wind.

TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning.

We report here new computational tools and strategies to efficiently generate three-dimensional models for oligomeric biomolecular complexes in cases where there is limited experimental restraint data to guide the docking calculations. Our computational tools are designed to rapidly and exhaustively enumerate all geometrically possible docking poses for an oligomeric complex, rather than generate detailed, atomic-resolution models. Experimental data, such as interatomic distance measurements, are then used to select and refine docking poses that are consistent with the experimental restraints. Our computational toolkit is designed for use with sparse data sets to generate intermediate-resolution docking models, and utilizes distance difference matrix analysis to identify further restraint measurements that will provide maximum additional structural refinement. Thus, these tools can be used to help plan optimal residue positions for probe incorporation in labor-intensive biophysical experiments such as chemical cross-linking, electron paramagnetic resonance, or Förster resonance energy transfer spectroscopy studies. We present benchmark results for docking the collection of all 176 heterodimer protein complexes from the ZDOCK database, as well as a protein homodimer with recently collected experimental distance restraints, to illustrate the toolkit's capabilities and performance, and to demonstrate how distance difference matrix analysis can automatically identify and prioritize additional restraint measurements that allow us to rapidly optimize docking poses.

Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals.

In this review, the strategies being employed to exploit the inherent durability of biofilms and the diverse nutrient cycling of the microbiome for bioremediation are explored. Focus will be given to halogenated compounds, hydrocarbons, pharmaceuticals, and personal care products as well as some heavy metals and toxic minerals, as these groups represent the majority of priority pollutants. For decades, industrial processes have been creating waste all around the world, resulting in contaminated sediments and subsequent, far-reaching dispersal into aquatic environments. As persistent pollutants have accumulated and are still being created and disposed, the incentive to find suitable and more efficient solutions to effectively detoxify the environment is even greater. Indigenous bacterial communities are capable of metabolizing persistent organic pollutants and oxidizing heavy metal contaminants. However, their low abundance and activity in the environment, difficulties accessing the contaminant or nutrient limitations in the environment all prevent the processes from occurring as quickly as desired and thus reaching the proposed clean-up goals. Biofilm communities provide among other things a beneficial structure, possibility for nutrient, and genetic exchange to participating microorganisms as well as protection from the surrounding environment concerning for instance predation and chemical and shear stresses. Biofilms can also be utilized in other ways as biomarkers for monitoring of stream water quality from for instance mine drainage. The durability and structure of biofilms together with the diverse array of structural and metabolic characteristics make these communities attractive actors in biofilm-mediated remediation solutions and ecosystem monitoring.

Ethics of clinical science in a public health emergency: drug discovery at the bedside.

Clinical research under the usual regulatory constraints may be difficult or even impossible in a public health emergency. Regulators must seek to strike a good balance in granting as wide therapeutic access to new drugs as possible at the same time as gathering sound evidence of safety and effectiveness. To inform current policy, I reexamine the philosophical rationale for restricting new medicines to clinical trials, at any stage and for any population of patients (which resides in the precautionary principle), to show that its objective to protect public health, now or in the future, could soon be defeated in a pandemic. Providing wider therapeutic access and coordinating observations and natural experiments, including service delivery by cluster (wedged cluster trials), may provide such a balance. However, there are important questions of fairness to resolve before any such research can proceed.

Recently Emerged Novel Henipa-like Viruses: Shining a Spotlight on the Shrew.

Henipaviruses are zoonotic viruses, including some highly pathogenic and capable of serious disease and high fatality rates in both animals and humans. Hendra virus and Nipah virus are the most notable henipaviruses, resulting in significant outbreaks across South Asia, South-East Asia, and Australia. Pteropid fruit bats have been identified as key zoonotic reservoirs; however, the increased discovery of henipaviruses outside the geographic distribution of Pteropid fruit bats and the detection of novel henipa-like viruses in other species such as the shrew, rat, and opossum suggest that Pteropid bats are not the sole reservoir for henipaviruses. In this review, we provide an update on henipavirus spillover events and describe the recent detection of novel unclassified henipaviruses, with a strong focus on the shrew and its emerging role as a key host of henipaviruses.

Perceived coercion, perceived pressures and procedural justice arising from global lockdowns during the COVID-19 pandemic: A scoping review.

This aim of this scoping review is to map what is known about perceived coercion, perceived pressures and procedural justice within the context of the general population's experience of 'lockdowns' imposed by governments worldwide in response to the increased transmission of COVID-19. Arksey & O'Malley's (2005) framework for conducting scoping reviews was chosen. A sensitive search strategy was devised and conducted using PubMed, Scopus, and Web of Science using the following search terms: (adherence OR acceptance OR agreement OR trust OR distrust OR compliance OR willing*) OR (perceived coerc* OR percept* coerc* OR pressure OR force OR influence OR control OR threat OR justice) AND (lockdown) AND (COVID OR SARS-CoV-2 OR COVID-19). The database search initially produced 41,628 articles to screen. A total of 40 articles were included in this review and the following five themes were identified from the studies: perceived acceptability and willingness to adhere to lockdown; perceived control during lockdown; perceived pressures arising from lockdown; perceived threat of sanction from others and the procedural (in)justice of lockdown. Our synthesis suggests that i) individuals experienced an initial willingness and tolerance of lockdown that lessened over time as perceptions of personal control decreased; ii) that social influences may pressure individuals to follow or break lockdown rules; and iii) that justifiability and proportionality together with individuals' perceptions of harm from COVID-19 may impact the extent to which individuals adhere to lockdown. Furthermore, the review found an absence of information regarding specific individual characteristics and circumstances that increase the likelihood of experiencing perceived coercion and its related constructs and highlights a need for a better understanding of the cultural and socioeconomic factors affecting perceptions of, and adherence to, lockdown.

Is equipoise a useful concept to justify randomised controlled trials in the cultural context of Pakistan? A survey of clinicians in relation to a trial of talking therapy for young people who self-harm.

BACKGROUND: Clinical equipoise, also defined as the uncertainty principle, is considered essential when recruiting subjects to a clinical trial. However, equipoise is threatened when clinicians are influenced by their own preferences. Little research has investigated equipoise in the context of trial recruitment. METHODS: This cross-sectional survey sought clinicians' views (operationalised as 11 statements relating to treatments offered in a trial of a psychological intervention for young people) about equipoise and individual treatment preferences in the context of moral justification for recruiting young people at risk of self-harm or suicide to a randomised controlled trial (RCT) to evaluate the Youth Culturally Adapted Manual Assisted Psychological Intervention (Y-CMAP) in Pakistan. We compared the views of clinicians involved in Y-CMAP RCT recruitment to those of a sample of clinicians not involved in trial recruitment but treating similar patients, comparing their sociodemographic characteristics and the proportions of those in each group agreeing with each statement. RESULTS: There was a response rate of 96% (75/78). Findings showed that, during trial recruitment and before the RCT results were known, the majority of all responding clinicians (73.3%) considered Y-CMAP to be an effective treatment for young people at risk of self-harm or suicide. Although there was an acknowledgement of individual preferences for the intervention, there was near consensus (90%) on the need to conduct an RCT for reaching an evidence-based decision. However, there were no significant differences in the proportion of recruiting clinicians reporting a treatment preference for Y-CMAP than non-recruiting clinicians (31 (88.6%) versus 36 (90%), p = 0.566). A significantly higher proportion of non-recruiting clinicians (87.5%) as compared to (48.5%) in the trial (p = 0.000) stated that there may be other treatments that may be equally good for the patients, seemingly undermining a preference for the intervention. Those reporting a treatment preference also acknowledged that there was nothing on which this preference was based, however confident they felt about them, thus accepting clinical equipoise as ethical justification for conducting the RCT. There was a significant group difference in views that treatment overall is better as a result of young patients' participation in the Y-CMAP trial (p = 0.015) (i.e. more clinicians not involved in the trial agreed with this statement). Similarly, more clinicians not involved in the trial agreed on the perceived availability of other treatment options that were good for young people at risk of self-harm (p < 0.05). CONCLUSIONS: The paper highlights that clinicians in Pakistan accept the notion of clinical equipoise as an ethical justification for patient participation in RCTs. The need for conducting RCTs to generate evidence base and to reduce bias was considered important by the clinical community.

Henipavirus-induced neuropathogenesis in mice.

Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses that can cause fatal encephalitis in humans. Many animal models have been used to study henipavirus pathogenesis. In the mouse, HeV infection has previously shown that intranasal challenge can lead to neurological infection, however mice similarly challenged with NiV show no evidence of virus infecting the brain. We generated recombinant HeV (rHeV) and NiV (rNiV) where selected proteins were switched to examine their role in neuroinvasion in the mouse. These viruses displayed similar growth kinetics when compared to wildtype in vitro. In the mouse, infection outcomes with recombinant virus did not differ to infection outcomes of wildtype viruses. Virus was detected in the brain of 5/30 rHeV-challenged mice, but not rNiV-challenged mice. To confirm the permissiveness of mouse neurons to these viruses, primary mouse neurons were successfully infected in vitro, suggesting that other pathobiological factors contribute to the differences in disease outcomes in mice.

Determination of structural models of the complex between the cytoplasmic domain of erythrocyte band 3 and ankyrin-R repeats 13-24.

The adaptor protein ankyrin-R interacts via its membrane binding domain with the cytoplasmic domain of the anion exchange protein (AE1) and via its spectrin binding domain with the spectrin-based membrane skeleton in human erythrocytes. This set of interactions provides a bridge between the lipid bilayer and the membrane skeleton, thereby stabilizing the membrane. Crystal structures for the dimeric cytoplasmic domain of AE1 (cdb3) and for a 12-ankyrin repeat segment (repeats 13-24) from the membrane binding domain of ankyrin-R (AnkD34) have been reported. However, structural data on how these proteins assemble to form a stable complex have not been reported. In the current studies, site-directed spin labeling, in combination with electron paramagnetic resonance (EPR) and double electron-electron resonance, has been utilized to map the binding interfaces of the two proteins in the complex and to obtain inter-protein distance constraints. These data have been utilized to construct a family of structural models that are consistent with the full range of experimental data. These models indicate that an extensive area on the peripheral domain of cdb3 binds to ankyrin repeats 18-20 on the top loop surface of AnkD34 primarily through hydrophobic interactions. This is a previously uncharacterized surface for binding of cdb3 to AnkD34. Because a second dimer of cdb3 is known to bind to ankyrin repeats 7-12 of the membrane binding domain of ankyrin-R, the current models have significant implications regarding the structural nature of a tetrameric form of AE1 that is hypothesized to be involved in binding to full-length ankyrin-R in the erythrocyte membrane.

Hard paternalism, fairness and clinical research: why not?

Jansen and Wall suggest a new way of defending hard paternalism in clinical research. They argue that non-therapeutic research exposing people to more than minimal risk should be banned on egalitarian grounds: in preventing poor decision-makers from making bad decisions, we will promote equality of welfare. We argue that their proposal is flawed for four reasons. First, the idea of poor decision-makers is much more problematic than Jansen and Wall allow. Second, pace Jansen and Wall, it may be practicable for regulators to uncover the values that a potential research participant holds when agreeing to enter a research project, so their claim that we must ban such research projects for all if we are to ban them for poor decision-makers looks to be unmotivated. Third, there seem to be cases where the liberty to enter the sort of research project Jansen and Wall discuss is morally weighty, and arguably should outweigh concerns of egalitarian distribution. Fourth, banning certain types of research, which seem on the face of it to offer an unfavourable risk-benefit ratio, would have unwelcome consequences for all clinical research, which Jansen and Wall do not recognize.

A qualitative investigation of selecting surrogate decision-makers.

BACKGROUND: Empirical studies of surrogate decision-making tend to assume that surrogates should make only a 'substituted judgement'--that is, judge what the patient would want if they were mentally competent. OBJECTIVES: To explore what people want in a surrogate decision-maker whom they themselves select and to test the assumption that people want their chosen surrogate to make only a substituted judgement. METHODS: 30 undergraduate students were recruited. They were presented with a hypothetical scenario about their expected loss of mental capacity in the future and asked to answer some questions about their choice of surrogate. These data were analysed qualitatively using thematic content analysis. RESULTS: Most respondents talked about choosing someone who was caring and competent in certain ways, giving interesting evidence for their judgements. Surprisingly few highlighted how well they thought their chosen surrogate knew their preferences and would be able to make a substituted judgement. Moreover, few specified that their chosen surrogate had similar attitudes and values to their own and so would make a similar decision to theirs in the circumstances presented. Some respondents also referred to the social role of their chosen surrogate or the social dynamics of their situation which influenced their choices, as well as to ideas of reciprocity and characteristics of honesty and loyalty. CONCLUSION: In the event that they lose mental capacity, many people will not select a surrogate to decide about medical treatments on their behalf solely on the basis that they expect their surrogate to make a substituted judgement.

Assessing the remedy: the case for contracts in clinical trials.

Current orthodoxy in research ethics assumes that subjects of clinical trials reserve rights to withdraw at any time and without giving any reason. This view sees the right to withdraw as a simple extension of the right to refuse to participate all together. In this paper, however, I suggest that subjects should assume some responsibilities for the internal validity of the trial at consent and that these responsibilities should be captured by contract. This would allow the researcher to impose a penalty on the subject if he were to withdraw without good reason and on a whim. This proposal still leaves open the possibility of withdrawing without penalty when it is in the subject's best interests to do so. Giving researchers recourse to legal remedy may now be necessary to protect the science, as existing methods used to increase retention are inadequate for one reason or another.

Evaluation of henipavirus chemical inactivation methods for the safe removal of samples from the high-containment PC4 laboratory.

Henipaviruses, Hendra (HeV) and Nipah (NiV), are highly pathogenic zoonotic agents that pose a serious health risk to human life, and as such are restricted to physical containment 4 (PC4) laboratories. For further analysis of virus-infected biological specimens, it is necessary to ensure absolute inactivation of any infectious virus present before removal from the PC4 laboratory. To evaluate the inactivation of HeV and NiV within infected samples, two chemical inactivation methods were assessed. Henipavirus-infected cell monolayers treated with 4 % paraformaldehyde (PFA) showed the complete inactivation of infectious virus, with an inactivation period of 15 min resulting in more than 8-log decrease in infectious titre. NiV-infected tissue samples treated with 10 % neutral-buffered formalin (NBF) showed a complete reduction of infectious virus in 7/8 ferret organs incubated for 24 h, with the remaining tissue demonstrating complete virus inactivation after 48 h. The chemical inactivation methods described herein evaluated two simple methods of henipavirus inactivation, resulting in the complete inactivation of infectious virus - an essential requirement for the safe removal and handling of biological samples from the PC4 laboratory.

Analysis of kinetic isotope effects for proton-coupled electron transfer reactions.

A series of rate constant expressions for nonadiabatic proton-coupled electron transfer (PCET) reactions are analyzed and compared. The approximations underlying each expression are enumerated, and the regimes of validity for each expression are illustrated by calculations on model systems. In addition, the kinetic isotope effects (KIEs) for a series of model PCET reactions are analyzed to elucidate the fundamental physical principles dictating the magnitude of the KIE and the dependence of the KIE on the physical properties of the system, including temperature, reorganization energy, driving force, equilibrium proton donor-acceptor distance, and effective frequency of the proton donor-acceptor mode. These calculations lead to three physical insights that are directly relevant to experimental data. First, these calculations provide an explanation for a decrease in the KIE as the proton donor-acceptor distance increases, even though typically the KIE will increase with increasing equilibrium proton donor-acceptor distance if all other parameters remain fixed. Often the proton donor-acceptor frequency decreases as the proton donor-acceptor distance increases, and these two effects impact the KIE in opposite directions, so either trend could be observed. Second, these calculations provide an explanation for an increase in the KIE as the temperature increases, even though typically the KIE will decrease with increasing temperature if all other parameters remain fixed. The combination of a rigid hydrogen bond, which corresponds to a high proton donor-acceptor frequency, and low solvent polarity, which corresponds to small solvent reorganization energy, allows the KIE to either increase or decrease with temperature, depending on the other properties of the system. Third, these calculations provide insight into the dependence of the rate constant and KIE on the driving force, which has been studied experimentally for a wide range of PCET systems. The rate constant increases as the driving force becomes more negative because excited vibronic product states associated with low free energy barriers and relatively large vibronic couplings become accessible. The ln[KIE] has a maximum near zero driving force and decreases significantly as the driving force becomes more positive or negative because the contributions from excited vibronic states increase as the reaction becomes more asymmetric, and contributions from excited vibronic states decrease the KIE. These calculations and analyses lead to experimentally testable predictions of trends in the KIEs for PCET systems.