A quantum coherent spin in hexagonal boron nitride at ambient conditions.

Solid-state spin-photon interfaces that combine single-photon generation and long-lived spin coherence with scalable device integration-ideally under ambient conditions-hold great promise for the implementation of quantum networks and sensors. Despite rapid progress reported across several candidate systems, those possessing quantum coherent single spins at room temperature remain extremely rare. Here we report quantum coherent control under ambient conditions of a single-photon-emitting defect spin in a layered van der Waals material, namely, hexagonal boron nitride. We identify that the carbon-related defect has a spin-triplet electronic ground-state manifold. We demonstrate that the spin coherence is predominantly governed by coupling to only a few proximal nuclei and is prolonged by decoupling protocols. Our results serve to introduce a new platform to realize a room-temperature spin qubit coupled to a multiqubit quantum register or quantum sensor with nanoscale sample proximity.

Interspecies Transmission of Swine Influenza A Viruses and Human Seasonal Vaccine-Mediated Protection Investigated in Ferret Model.

We investigated the infection dynamics of 2 influenza A(H1N1) virus isolates from the swine 1A.3.3.2 (pandemic 2009) and 1C (Eurasian, avian-like) lineages. The 1C-lineage virus, A/Pavia/65/2016, although phylogenetically related to swine-origin viruses, was isolated from a human clinical case. This strain infected ferrets, a human influenza model species, and could be transmitted by direct contact and, less efficiently, by airborne exposure. Infecting ferrets and pigs (the natural host) resulted in mild or inapparent clinical signs comparable to those observed with 1A.3.3.2-lineage swine-origin viruses. Both H1N1 viruses could infect pigs and were transmitted to cohoused ferrets. Ferrets vaccinated with a human 2016-17 seasonal influenza vaccine were protected against infection with the antigenically matched 1A pandemic 2009 virus but not against the swine-lineage 1C virus. Our results reaffirm the need for continuous influenza A virus surveillance in pigs and identification of candidate human vaccine viruses.

Comparing Additionality of Tuberculosis Cases Using GeneXpert or Smear-Based Active TB Case-Finding Strategies among Social Contacts of Index Cases in Nepal.

This study compares the yield and additionality of community-based active tuberculosis (TB) active case-finding strategies using either smear microscopy or GeneXpert as the TB diagnostic test. Active case-finding strategies screened social contacts of index cases and high-risk groups in four districts of Nepal in July 2017-2019. Two districts (Chitwan and Dhanusha) applied GeneXpert testing and two districts (Makwanpur and Mahotarri) used smear microscopy. Two control districts implemented standard national TB program activities. Districts implementing GeneXpert testing screened 23,657 people for TB, tested 17,114 and diagnosed 764 TB cases, producing a yield of 4.5%. Districts implementing smear microscopy screened 19,961 people for TB, tested 13,285 and diagnosed 437 cases, producing a yield of 3.3%. The screening numbers required were 31 for GeneXpert and 45.7 for smear districts. The test numbers required were 22.4 and 30.4 for GeneXpert and smear. Using the TB REACH additionality method, social contact tracing for TB through GeneXpert testing contributed to a 20% (3958/3322) increase in district-level TB notifications, smear microscopy 12.4% (3146/2798), and -0.5% (2553/2566) for control districts. Therefore, social contact tracing of TB index cases using GeneXpert testing should be implemented throughout Nepal within the TB FREE initiative to close the notification gap and accelerate progress toward END TB strategy targets.

JMM Profile: Swine influenza A virus: a neglected virus with pandemic potential.

Swine influenza is an acute respiratory disease of swine caused by swine influenza A virus (SwIAV). The ability of SwIAV to spread bidirectionally from animals to humans (zoonotic), and from humans to animals (reverse zoonotic), drives coinfection that can result in gene segment exchange and elevates the risk of generating viruses with pandemic potential. Compared to human-origin influenza A viruses, current data indicate a greater diversity amongst circulating SwIAVs, with three major subtypes (classified by haemagglutinin and neuraminidase) circulating globally in swine (H1N1, H1N2 and H3N2). The lack of protection afforded by human seasonal influenza vaccines against SwIAVs exacerbates the risk associated with reassortment of human, swine and potentially avian viruses. As such, global monitoring of SwIAVs is important for both human and animal health as they represent a true 'One Health' challenge with pandemic potential.

Coherence protection of spin qubits in hexagonal boron nitride.

Spin defects in foils of hexagonal boron nitride are an attractive platform for magnetic field imaging, since the probe can be placed in close proximity to the target. However, as a III-V material the electron spin coherence is limited by the nuclear spin environment, with spin echo coherence times of ∽100 ns at room temperature accessible magnetic fields. We use a strong continuous microwave drive with a modulation in order to stabilize a Rabi oscillation, extending the coherence time up to ∽ 4µs, which is close to the 10 µs electron spin lifetime in our sample. We then define a protected qubit basis, and show full control of the protected qubit. The coherence times of a superposition of the protected qubit can be as high as 0.8 µs. This work establishes that boron vacancies in hexagonal boron nitride can have electron spin coherence times that are competitive with typical nitrogen vacancy centres in small nanodiamonds under ambient conditions.

A systematic review of strategies adopted to scale up COVID-19 testing in low-, middle- and high-income countries.

OBJECTIVE: We undertook a systematic review of strategies adopted to scale up COVID-19 testing in countries across income levels to identify successful approaches and facilitate learning. METHODS: Scholarly articles in English from PubMed, Google scholar and Google search engine describing strategies used to increase COVID-19 testing in countries were reviewed. Deductive analysis to allocate relevant text from the reviewed publications/reports to the a priori themes was done. MAIN RESULTS: The review covered 32 countries, including 11 high-income, 2 upper-middle-income, 13 lower-middle-income and 6 low-income countries. Most low- and middle-income countries (LMICs) increased the number of laboratories available for testing and deployed sample collection and shipment to the available laboratories. The high-income countries (HICs) that is, South Korea, Germany, Singapore and USA developed molecular diagnostics with accompanying regulatory and legislative framework adjustments to ensure the rapid development and use of the tests. HICs like South Korea leveraged existing manufacturing systems to develop tests, while the LMICs leveraged existing national disease control programmes (HIV, tuberculosis, malaria) to increase testing. Continent-wide, African Centres for Disease Control and Prevention-led collaborations increased testing across most African countries through building capacity by providing testing kits and training. CONCLUSION: Strategies taken appear to reflect the existing systems or economies of scale that a particular country could leverage. LMICs, for example, drew on the infectious disease control programmes already in place to harness expertise and laboratory capacity for COVID-19 testing. There however might have been strategies adopted by other countries but were never published and thus did not appear anywhere in the searched databases.

Excited State Spectroscopy of Boron Vacancy Defects in Hexagonal Boron Nitride Using Time-Resolved Optically Detected Magnetic Resonance.

We report optically detected magnetic resonance (ODMR) measurements of an ensemble of spin-1 negatively charged boron vacancies in hexagonal boron nitride. The photoluminescence decay rates are spin-dependent, with intersystem crossing rates of 1.02 ns-1 and 2.03 ns-1 for the mS = 0 and mS = ±1 states, respectively. Time gating the photoluminescence enhances the ODMR contrast by discriminating between different decay rates. This is particularly effective for detecting the spin of the optically excited state, where a zero-field splitting of |DES| = 2.09 GHz is measured. The magnetic field dependence of the photoluminescence exhibits dips corresponding to the ground (GSLAC) and excited-state (ESLAC) anticrossings and additional anticrossings due to coupling with nearby spin-1/2 parasitic impurities. Comparison to a model suggests that the anticrossings are mediated by the interaction with nuclear spins and allows an estimate of the ratio of the singlet to triplet spin-dependent relaxation rates of κ0/κ1 = 0.34.

Stimulated Emission Depletion Spectroscopy of Color Centers in Hexagonal Boron Nitride.

We demonstrate the use of Stimulated Emission Depletion (STED) spectroscopy to map the electron-optical-phonon sideband of the ground state of the radiative transition of color centers in hexagonal boron nitride emitting at 2.0-2.2 eV, with in-plane linear polarization. The measurements are compared to photoluminescence of excitation (PLE) spectra that maps the electron-optical-phonon sideband of the excited state. The main qualitative difference is a red-shift in the longitudinal optical phonon peak associated with E 1u symmetry at the zone center. We compare our results to theoretical work on different defect species in hBN and find they are consistent with a carbon-based defect.

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions.

Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research. We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links.

Comparative Yield of Tuberculosis during Active Case Finding Using GeneXpert or Smear Microscopy for Diagnostic Testing in Nepal: A Cross-Sectional Study.

This study compared the yield of tuberculosis (TB) active case finding (ACF) interventions applied under TB REACH funding. Between June 2017 to November 2018, Birat Nepal Medical Trust identified presumptive cases using simple verbal screening from three interventions: door-to-door screening of social contacts of known index cases, TB camps in remote areas, and screening for hospital out-patient department (OPD) attendees. Symptomatic individuals were then tested using smear microscopy or GeneXpert MTB/RIF as first diagnostic test. Yield rates were compared for each intervention and diagnostic method. We evaluated additional cases notified from ACF interventions by comparing case notifications of the intervention and control districts using standard TB REACH methodology. The project identified 1092 TB cases. The highest yield was obtained from OPD screening at hospitals (n = 566/1092; 52%). The proportion of positive tests using GeneXpert (5.5%, n = 859/15,637) was significantly higher than from microscopy testing 2% (n = 120/6309). (OR = 1.4; 95%CI = 1.12-1.72; p = 0.0026). The project achieved 29% additionality in case notifications in the intervention districts demonstrating that GeneXpert achieved substantially higher case-finding yields. Therefore, to increase national case notification for TB, Nepal should integrate OPD screening using GeneXpert testing in every district hospital and scale up of community-based ACF of TB patient contacts nationally.

Comparative Metabologenomics Analysis of Polar Actinomycetes.

Biosynthetic and chemical datasets are the two major pillars for microbial drug discovery in the omics era. Despite the advancement of analysis tools and platforms for multi-strain metabolomics and genomics, linking these information sources remains a considerable bottleneck in strain prioritisation and natural product discovery. In this study, molecular networking of the 100 metabolite extracts derived from applying the OSMAC approach to 25 Polar bacterial strains, showed growth media specificity and potential chemical novelty was suggested. Moreover, the metabolite extracts were screened for antibacterial activity and promising selective bioactivity against drug-persistent pathogens such as Klebsiella pneumoniae and Acinetobacter baumannii was observed. Genome sequencing data were combined with metabolomics experiments in the recently developed computational approach, NPLinker, which was used to link BGC and molecular features to prioritise strains for further investigation based on biosynthetic and chemical information. Herein, we putatively identified the known metabolites ectoine and chrloramphenicol which, through NPLinker, were linked to their associated BGCs. The metabologenomics approach followed in this study can potentially be applied to any large microbial datasets for accelerating the discovery of new (bioactive) specialised metabolites.

Vaccines That Reduce Viral Shedding Do Not Prevent Transmission of H1N1 Pandemic 2009 Swine Influenza A Virus Infection to Unvaccinated Pigs.

Swine influenza A virus (swIAV) infection causes substantial economic loss and disease burden in humans and animals. The 2009 pandemic H1N1 (pH1N1) influenza A virus is now endemic in both populations. In this study, we evaluated the efficacy of different vaccines in reducing nasal shedding in pigs following pH1N1 virus challenge. We also assessed transmission from immunized and challenged pigs to naive, directly in-contact pigs. Pigs were immunized with either adjuvanted, whole inactivated virus (WIV) vaccines or virus-vectored (ChAdOx1 and MVA) vaccines expressing either the homologous or heterologous influenza A virus hemagglutinin (HA) glycoprotein, as well as an influenza virus pseudotype (S-FLU) vaccine expressing heterologous HA. Only two vaccines containing homologous HA, which also induced high hemagglutination inhibitory antibody titers, significantly reduced virus shedding in challenged animals. Nevertheless, virus transmission from challenged to naive, in-contact animals occurred in all groups, although it was delayed in groups of vaccinated animals with reduced virus shedding.IMPORTANCE This study was designed to determine whether vaccination of pigs with conventional WIV or virus-vectored vaccines reduces pH1N1 swine influenza A virus shedding following challenge and can prevent transmission to naive in-contact animals. Even when viral shedding was significantly reduced following challenge, infection was transmissible to susceptible cohoused recipients. This knowledge is important to inform disease surveillance and control strategies and to determine the vaccine coverage required in a population, thereby defining disease moderation or herd protection. WIV or virus-vectored vaccines homologous to the challenge strain significantly reduced virus shedding from directly infected pigs, but vaccination did not completely prevent transmission to cohoused naive pigs.

How to reduce household costs for people with tuberculosis: a longitudinal costing survey in Nepal.

The aim of this study was to compare costs and socio-economic impact of tuberculosis (TB) for patients diagnosed through active (ACF) and passive case finding (PCF) in Nepal. A longitudinal costing survey was conducted in four districts of Nepal from April 2018 to October 2019. Costs were collected using the WHO TB Patient Costs Survey at three time points: intensive phase of treatment, continuation phase of treatment and at treatment completion. Direct and indirect costs and socio-economic impact (poverty headcount, employment status and coping strategies) were evaluated throughout the treatment. Prevalence of catastrophic costs was estimated using the WHO threshold. Logistic regression and generalized estimating equation were used to evaluate risk of incurring high costs, catastrophic costs and socio-economic impact of TB over time. A total of 111 ACF and 110 PCF patients were included. ACF patients were more likely to have no education (75% vs 57%, P = 0.006) and informal employment (42% vs 24%, P = 0.005) Compared with the PCF group, ACF patients incurred lower costs during the pretreatment period (mean total cost: US$55 vs US$87, P < 0.001) and during the pretreatment plus treatment periods (mean total direct costs: US$72 vs US$101, P < 0.001). Socio-economic impact was severe for both groups throughout the whole treatment, with 32% of households incurring catastrophic costs. Catastrophic costs were associated with 'no education' status [odds ratio = 2.53(95% confidence interval = 1.16-5.50)]. There is a severe and sustained socio-economic impact of TB on affected households in Nepal. The community-based ACF approach mitigated costs and reached the most vulnerable patients. Alongside ACF, social protection policies must be extended to achieve the zero catastrophic costs milestone of the End TB strategy.

Towards harmonization of microscopy methods for malaria clinical research studies.

Microscopy performed on stained films of peripheral blood for detection, identification and quantification of malaria parasites is an essential reference standard for clinical trials of drugs, vaccines and diagnostic tests for malaria. The value of data from such research is greatly enhanced if this reference standard is consistent across time and geography. Adherence to common standards and practices is a prerequisite to achieve this. The rationale for proposed research standards and procedures for the preparation, staining and microscopic examination of blood films for malaria parasites is presented here with the aim of improving the consistency and reliability of malaria microscopy performed in such studies. These standards constitute the core of a quality management system for clinical research studies employing microscopy as a reference standard. They can be used as the basis for the design of training and proficiency testing programmes as well as for procedures and quality assurance of malaria microscopy in clinical research.

Efficient human-machine control with asymmetric marginal reliability input devices.

Input devices such as motor-imagery brain-computer interfaces (BCIs) are often unreliable. In theory, channel coding can be used in the human-machine loop to robustly encapsulate intention through noisy input devices but standard feedforward error correction codes cannot be practically applied. We present a practical and general probabilistic user interface for binary input devices with very high noise levels. Our approach allows any level of robustness to be achieved, regardless of noise level, where reliable feedback such as a visual display is available. In particular, we show efficient zooming interfaces based on feedback channel codes for two-class binary problems with noise levels characteristic of modalities such as motor-imagery based BCI, with accuracy <75%. We outline general principles based on separating channel, line and source coding in human-machine loop design. We develop a novel selection mechanism which can achieve arbitrarily reliable selection with a noisy two-state button. We show automatic online adaptation to changing channel statistics, and operation without precise calibration of error rates. A range of visualisations are used to construct user interfaces which implicitly code for these channels in a way that it is transparent to users. We validate our approach with a set of Monte Carlo simulations, and empirical results from a human-in-the-loop experiment showing the approach operates effectively at 50-70% of the theoretical optimum across a range of channel conditions.

Optical Gating of Photoluminescence from Color Centers in Hexagonal Boron Nitride.

We report on multicolor excitation experiments with color centers in hexagonal boron nitride at cryogenic temperatures. We demonstrate controllable optical switching between bright and dark states of color centers emitting around 2 eV. Resonant, or quasi-resonant, excitation of photoluminescence also pumps the color center, via a two-photon process, into a dark state, where it becomes trapped. Repumping back into the bright state has a step-like spectrum with a defect-dependent threshold between 2.25 and 2.6 eV. This behavior is consistent with photoionization and charging between optically bright and dark states of the defect. Furthermore, a second zero phonon line, detuned by +0.4 eV, is observed in absorption with orthogonal polarization to the emission, evidencing an additional energy level in the color center.

Transmission dynamics between infected waterfowl and terrestrial poultry: Differences between the transmission and tropism of H5N8 highly pathogenic avian influenza virus (clade 2.3.4.4a) among ducks, chickens and turkeys.

H5N8 highly-pathogenic avian influenza viruses (HPAIVs, clade 2.3.4.4) have spread globally via migratory waterfowl. Pekin ducks infected with a UK virus (H5N8-2014) served as the donors of infection in three separate cohousing experiments to attempt onward transmission chains to sequentially introduced groups of contact ducks, chickens and turkeys. Efficient transmission occurred among ducks and turkeys up to the third contact stage, with all (100%) birds becoming infected. Introduction of an additional fourth contact group of ducks to the turkey transmission chain demonstrated retention of H5N8-2014's waterfowl-competent adaptation. However, onward transmission ceased in chickens at the second contact stage where only 13% became infected. Analysis of viral progeny at this contact stage revealed no emergent polymorphisms in the intra-species (duck) transmission chain, but both terrestrial species included changes in the polymerase and accessory genes. Typical HPAIV pathogenesis and mortality occurred in infected chickens and turkeys, contrasting with 5% mortality among ducks.

The role of active case finding in reducing patient incurred catastrophic costs for tuberculosis in Nepal.

BACKGROUND: The World Health Organization (WHO) End TB Strategy has established a milestone to reduce the number of tuberculosis (TB)- affected households facing catastrophic costs to zero by 2020. The role of active case finding (ACF) in reducing patient costs has not been determined globally. This study therefore aimed to compare costs incurred by TB patients diagnosed through ACF and passive case finding (PCF), and to determine the prevalence and intensity of patient-incurred catastrophic costs in Nepal. METHODS: The study was conducted in two districts of Nepal: Bardiya and Pyuthan (Province No. 5) between June and August 2018. One hundred patients were included in this study in a 1:1 ratio (PCF: ACF, 25 consecutive ACF and 25 consecutive PCF patients in each district). The WHO TB patient costing tool was applied to collect information from patients or a member of their family regarding indirect and direct medical and non-medical costs. Catastrophic costs were calculated based on the proportion of patients with total costs exceeding 20% of their annual household income. The intensity of catastrophic costs was calculated using the positive overshoot method. The chi-square and Wilcoxon-Mann-Whitney tests were used to compare proportions and costs. Meanwhile, the Mantel Haenszel test was performed to assess the association between catastrophic costs and type of diagnosis. RESULTS: Ninety-nine patients were interviewed (50 ACF and 49 PCF). Patients diagnosed through ACF incurred lower costs during the pre-treatment period (direct medical: USD 14 vs USD 32, P = 0.001; direct non-medical: USD 3 vs USD 10, P = 0.004; indirect, time loss: USD 4 vs USD 13, P <  0.001). The cost of the pre-treatment and intensive phases combined was also lower for direct medical (USD 15 vs USD 34, P = 0.002) and non-medical (USD 30 vs USD 54, P = 0.022) costs among ACF patients. The prevalence of catastrophic direct costs was lower for ACF patients for all thresholds. A lower intensity of catastrophic costs was also documented for ACF patients, although the difference was not statistically significant. CONCLUSIONS: ACF can reduce patient-incurred costs substantially, contributing to the End TB Strategy target. Other synergistic policies, such as social protection, will also need to be implemented to reduce catastrophic costs to zero among TB-affected households.

Statistical modelling of data showing pandemic H1N1 2009 swine influenza a virus infection kinetics in vaccinated pigs.

A swine influenza A pandemic 2009 H1N1 (pH1N1) virus was used in a pig challenge model to investigate the efficacy of whole inactivated vaccines homologous or heterologous to the challenge virus as well as a commercial vaccine. Nasal shedding of viral RNA was monitored daily by real-time, quantitative RT-PCR (RRT-qPCR) as detailed (1). Here we report the statistical modelling of the viral RNA shedding kinetics.

Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes.

The membranes of the first protocells on the early Earth were likely self-assembled from fatty acids. A major challenge in understanding how protocells could have arisen and withstood changes in their environment is that fatty acid membranes are unstable in solutions containing high concentrations of salt (such as would have been prevalent in early oceans) or divalent cations (which would have been required for RNA catalysis). To test whether the inclusion of amino acids addresses this problem, we coupled direct techniques of cryoelectron microscopy and fluorescence microscopy with techniques of NMR spectroscopy, centrifuge filtration assays, and turbidity measurements. We find that a set of unmodified, prebiotic amino acids binds to prebiotic fatty acid membranes and that a subset stabilizes membranes in the presence of salt and Mg2+ Furthermore, we find that final concentrations of the amino acids need not be high to cause these effects; membrane stabilization persists after dilution as would have occurred during the rehydration of dried or partially dried pools. In addition to providing a means to stabilize protocell membranes, our results address the challenge of explaining how proteins could have become colocalized with membranes. Amino acids are the building blocks of proteins, and our results are consistent with a positive feedback loop in which amino acids bound to self-assembled fatty acid membranes, resulting in membrane stabilization and leading to more binding in turn. High local concentrations of molecular building blocks at the surface of fatty acid membranes may have aided the eventual formation of proteins.