Search

Successful supervision is broad-based and collegial, and positively affects both teaching and learning. Successful teaching is characterized by professional decision making facilitated by supportive supervision. The most powerful type of learning is student-driven, teacher-facilitated learning. Successful supervision, teaching, and learning are congruent and reflect one another, creating a "hall of mirrors." Supervision, teaching, and learning can both contribute to and flourish across 10 dimensions of successful schools, including care, service, trust, democratic community, equity grounded in equality, justice and peace, symbols and ceremonies, freedom and creativity, holistic development, and school vision. Reviews of literature on the dimensions of successful schools indicate a variety of positive benefits for schools, teachers, and students.

This article reports on a study of the value master’s students in a principal preparation program placed on a variety of instructional strategies. The aspiring principals completed a survey with fixed-response and open-ended items. The students’ most valued class discussions were about how their personal experiences related to the class topic and how to apply the topic to practice. The class activities they valued the most highly were problem solving, simulations, small-group discussions, and whole-group discussions. The highest rated out-of-class assignments included writing reflective papers, conducting interviews and observations, and performing leadership activities in schools. The types of readings the master’s students most appreciated were case studies and journal articles. In describing their “outstanding professor,” the aspiring principals focused on the professor’s personal qualities, creation of a positive learning environment, and constructivist teaching.

In response to sensory deprivation, the brain adapts according to contemporary demands to efficiently navigate a modified perceptual environment. This reorganization may result in improved processing of the remaining senses–a phenomenon referred to as compensatory crossmodal plasticity. One approach to explore this neuroplasticity is to consider the macrostructural changes in neural tissue that mirror this functional optimization. The current study is the first of its kind to measure MRI-derived gray matter (GM) volumes of control felines (n=30), while additionally identifying volumetric differences in response to perinatal deafness (30 ototoxically-deafened cats). To accomplish this purpose, regional and morphometric methods were performed in parallel. The regional analysis evaluated volumetric alterations of global GM, as well as the volumes of 146 regions of interest (ROIs) and 12 functional subgroupings of these ROIs. Results revealed whole-brain GM preservation; however, somatosensory and visual cortices exhibited an overall increase in volume. On a smaller scale, this analysis uncovered two auditory ROIs (second auditory cortex, A2, and ventral auditory field, VAF) that decreased in volume alongside two visual regions (anteromedial lateral suprasylvian area, AMLS and splenial visual area, SVA) that increased–all localized within the right hemisphere. Comparatively, the findings of tensor-based morphometry (TBM) generally aligned with those of the ROI-based method, as this voxel-wise approach demonstrated clusters of expansion coincident with visual- and somatosensory-related loci; although, it failed to detect any GM reductions following deafness. As distinct differences were identified in each analysis, the current study highlights the importance of employing multiple methods when exploring MRI volumetry. Overall, this study proposes that volumetric alterations within sensory loci allude to a redistribution of cortical space arising from modified perceptual demands following auditory deprivation.

Skull stripping is a fundamental preprocessing step in modern neuroimaging analyses that consists of removing non-brain voxels from structural images. When performed entirely manually, this laborious step can be rate-limiting for analyses, with the potential to influence the population size chosen. This emphasizes the need for a fully- or semi-automated masking procedure to decrease man-hours without an associated decline in accuracy. These algorithms are plentiful in human neuroimaging but are relatively lacking for the plethora of animal species used in research. Unfortunately, software designed for humans cannot be easily transformed for animal use due to the high amount of tailoring required to accurately account for the considerable degree of variation within the highly folded human cortex. As most animals have a relatively less complex cerebral morphology, intersubject variability is consequently decreased, presenting the possibility to simply warp the brain mask of a template image into subject space for the purpose of skull stripping. This study presents the use of the Cat Automated Registration-based Skull Stripper (CARSS) tool on feline structural images. Validation metrics revealed that this method was able to perform on par with manual raters on >90 % of scans tested, and that its consistency across multiple runs was superior to that of masking performed by two independent raters. Additionally, CARSS outperformed three well-known skull stripping programs on the validation dataset. Despite a handful of manual interventions required, the presented tool reduced the man-hours required to skull strip 60 feline images over tenfold when compared to a fully manual approach, proving to be invaluable for feline neuroimaging studies, particularly those with large population sizes.

In the absence of hearing, the plastic nature of the cerebral cortex allows select regions to be repurposed to serve the processing of remaining sensory modalities. This plasticity can be observed in many ways, including measuring the thickness differences of cortical gray matter between hearing and deaf populations to detect regional adaptations. In this study, T1-weighted images were acquired for hearing (n = 38) and perinatally-deafened (n = 31) cats using an ultra-high field 7T MRI scanner to identify normative feline cortical thickness, as well as areas of differing thickness between groups. Most significant changes to sensory-related regions demonstrated thicker cortices in the deaf compared to the hearing group, while specific non-sensory regions were found to be thinner. Furthermore, there was a modest lateralized component, finding that the gray matter of the left hemisphere was more susceptible to thickness changes following auditory deprivation. These results suggest distinct factors driving the adaptations in sensory versus non-sensory cortices in the brain following deafness, and reinforces the task-retainment model of crossmodal plasticity.

Objective: To date the vast majority of research in the visual neurosciences have been forced to adopt a highly constrained perspective of the vision system in which stimuli are processed in an open-loop reactive fashion (i.e., abrupt stimulus presentation followed by an evoked neural response). While such constraints enable high construct validity for neuroscientific investigation, the primary outcomes have been a reductionistic approach to isolate the component processes of visual perception. In electrophysiology, of the many neural processes studied under this rubric, the most well-known is, arguably, the P300 evoked response. There is, however, relatively little known about the real-world corollary of this component in free-viewing paradigms where visual stimuli are connected to neural function in a closed-loop. While growing evidence suggests that neural activity analogous to the P300 does occur in such paradigms, it is an open question when this response occurs and what behavioral or environmental factors could be used to isolate this component. Approach: The current work uses convolutional networks to decode neural signals during a free-viewing visual search task in a closed-loop paradigm within an open-world virtual environment. From the decoded activity we construct fixation-locked response profiles that enable estimations of the variable latency of any P300 analogue around the moment of fixation. We then use these estimates to investigate which factors best reduce variable latency and, thus, predict the onset time of the response. We consider measurable, search-related factors encompassing top-down (i.e., goal driven) and bottom-up (i.e., stimulus driven) processes, such as fixation duration and salience. We also consider saccade size as an intermediate factor reflecting the integration of these two systems. Main results: The results show that of these factors only saccade size reliably determines the onset time of P300 analogous activity for this task. Specifically, we find that for large saccades the variability in response onset is small enough to enable analysis using traditional ensemble averaging methods. Significance: The results show that P300 analogous activity does occur during closed-loop, free-viewing visual search while highlighting distinct differences between the open-loop version of this response and its real-world analogue. The results also further establish saccades, and saccade size, as a key factor in real-world visual processing.

Background Streptococcus pneumoniae is a major cause of morbidity and mortality from respiratory tract infections, pneumonia, meningitis, and sepsis. Nasopharyngeal carriage of pneumococcus is a prerequisite for pneumococcal disease and transmission. Since the global introduction of pneumococcal conjugated vaccines, rates of pneumococcal disease have declined for many vaccine type serotypes but serotype 3 (SPN3) continues to cause significant disease. The Experimental Human Pneumococcal Challenge (EHPC) model is a unique method of determining pneumococcal colonisation, understanding the impact of colonisation on acquired immunity and for testing pneumococcal vaccines. This study will develop a serotype 3 EHPC model to address some pertinent questions on the burden of pneumococcal disease in Malawi. Methods Healthy adults aged 18-50 years will be recruited, with a maximum target of 83 participants to complete all study visits. The study will consist of a dose ranging and safety study, followed by a reproducibility study. Sequential cohorts of 10 healthy participants will be challenged with escalating doses of SPN3 in the dose ranging study. Samples will be collected before inoculation and on days 2, 7, 13, 16, 21 and 28 following inoculations, for determination of carriage. A total of 33 participants will be enrolled in the reproducibility part and will use a dose that established ≥60% of carriage, and with a high safety profile. Samples will be collected for determination of both local and systemic immunological responses to pneumococcal challenge. Upon completion of study visits, participants will complete a questionnaire establish acceptability. Interpretations We expect to establish an optimal SPN3 dose required to establish nasopharyngeal colonisation in healthy adults in an EHPC model. The model can then be used to evaluate pneumococcal vaccines in both healthy and at-risk populations.

Sustainable structures are an important area of research, particularly for anticipated extended human presence on the Moon or Mars. Persistent human presence on the Moon will require building materials that are already present at the site to construct bases. The high cost associated with reinforcing metal (rebar) in mission payloads necessitates the exploration of alternative reinforcement methods for sustained lunar bases. Human hair is strong in tensile strength and will become available in any long-term mission. By using otherwise wasted hair instead of heavy metal, mission payloads and costs could be lowered. Concrete workability, compressive strength, and porosity were measured for a series of different cement compositions. These compositions consisted of combinations of Ordinary Portland Cement (OPC), lunar regolith, deionized (DI) water and human hair. Increased workability and porosity were found for increasing hair concentrations. Compressive strength slightly decreased with increased hair concentration.

Lanthipeptides are a large group of ribosomally encoded peptides cyclized by thioether and methylene bridges, which include the lantibiotics, lanthipeptides with antimicrobial activity. There are over 100 experimentally characterized lanthipeptides, with at least 25 distinct cyclization bridging patterns. We set out to understand the evolutionary dynamics and diversity of lanthipeptides. We identified 977 peptides in 2785 bacterial genomes from short open-reading frames encoding lanthipeptide modifiable amino acids (C, S and T) that lay chromosomally adjacent to genes encoding proteins containing the cyclase domain. These appeared to be synthesized by both known and novel enzymatic combinations. Our predictor of bridging topology suggested 36 novel-predicted topologies, including a single-cysteine topology seen in 179 lanthionine or labionin containing peptides, which were enriched for histidine. Evidence that supported the relevance of the single-cysteine containing lanthipeptide precursors included the presence of the labionin motif among single cysteine peptides that clustered with labionin-associated synthetase domains, and the leader features of experimentally defined lanthipeptides that were shared with single cysteine predictions. Evolutionary rate variation among peptide subfamilies suggests that selection pressures for functional change differ among subfamilies. Lanthipeptides that have recently evolved specific novel features may represent a richer source of potential novel antimicrobials, since their target species may have had less time to evolve resistance.

Tuberculosis (TB) caused 1.5 million deaths in 2020, making it the leading infectious killer after COVID-19. Bacille Calmette-Guerin (BCG) is the only licensed vaccine against TB but has sub-optimal efficacy against pulmonary TB and reduced effectiveness in regions close to the equator with high burden. Efforts to find novel vaccines are hampered due to the need for large-scale, prolonged, and costly clinical trials. Controlled human infection models (CHIMs) for TB may be used to accelerate vaccine development by ensuring only the most promising vaccine candidates are selected for phase 3 trials, but it is not currently possible to give participants Mycobacterium tuberculosis as a challenge agent. This study aims to replicate and refine an established BCG CHIM at the Liverpool School of Tropical Medicine. Participants will receive an intradermal injection with licensed BCG vaccine (Statens Serum Institut strain). In phase A, participants will undergo punch biopsy two weeks after administration, paired with minimally invasive methods of skin sampling (skin swab, microbiopsy, skin scrape). BCG detection by classical culture and molecular methods will be compared between these techniques and gold standard punch biopsy. Techniques meeting our pre-defined sensitivity and specificity criteria will be applied in Phase B to longitudinally assess intradermal BCG growth two, seven and fourteen days after administration. We will also measure compartmental immune responses in skin, blood and respiratory mucosa in Phase B. This feasibility study will transfer and refine an existing and safe model of BCG controlled human infection. Longitudinal BCG quantification has the potential to increase model sensitivity to detect vaccine and therapeutic responses. If successful, we aim to transfer the model to Malawi in future studies, a setting with endemic TB disease, to accelerate development of vaccines and therapeutics relevant for underserved populations who stand to benefit the most. Registration: ISRCTN: ISRCTN94098600 and ClinicalTrials.gov: NCT05820594

Direct Contact Membrane Distillation (DCMD) uses low heat sources to separate water from urea, which was then used as a plasticizer in regolith-based cement to make it more workable. The work investigated separating potable water and urea from artificial urine using DCMD and then characterizing the products. Water was successfully separated from the artificial urine solution as characterized by density, conductivity, pH, and substance concentrations. The concentrated urine solution was used in regolith-based cement cured under vacuum at temperatures that simulated temperatures that would be expected in construction on the Moon. Workability and other properties were improved by replacing water with concentrated urine solution in the mix.

The development of each nation is evaluated by its infrastructure, and each nation is competing with the others in infrastructure advancement, especially in the construction of roadways, since they play a vital role in the economic and social development of the nation. The conventional materials used for road construction are concrete and asphalt, which pose significant environmental challenges. This research gives insight into the potential of fly ash (FA) and corn stover (CS) in synthesizing geopolymer, as an alternative material for the construction of roads. This study examines the impact of three FA and CS mixture percentages and the particle size of CS on the compressive strength and porosity of geopolymer. The results indicate that incorporating larger amounts of CS in fly ash-based geopolymer may decrease the compressive strength of the geopolymer. Smaller CS particle sizes also tend to lead to lower compressive strength. Porosity of the geopolymer tended to increase with the incorporation of higher percentages of CS, particularly for smaller corn stover sizes. As a fine aggregate replacement for geopolymer, CS incorporation has the potential to reduce mined aggregate obtained from a process that harms the environment.

Background Hospital admission due to breathlessness carries a significant burden to patients and healthcare systems, particularly impacting people in low-income countries. Prompt appropriate treatment is vital to improve outcomes, but this relies on accurate diagnostic tests which are of limited availability in resource-constrained settings. We will provide an accurate description of acute breathlessness presentations in a multicentre prospective cohort study in Malawi, a low resource setting in Southern Africa, and explore approaches to strengthen diagnostic capacity. Objectives Primary objective: Delineate between causes of breathlessness among adults admitted to hospital in Malawi and report disease prevalence. Secondary objectives: Determine patient outcomes, including mortality and hospital readmission 90 days after admission; determine the diagnostic accuracy of biomarkers to differentiate between heart failure and respiratory infections (such as pneumonia) including brain natriuretic peptides, procalcitonin and C-reactive protein. Methods This is a prospective longitudinal cohort study of adults (≥18 years) admitted to hospital with breathlessness across two hospitals: 1) Queen Elizabeth Central Hospital, Blantyre, Malawi; 2) Chiradzulu District Hospital, Chiradzulu, Malawi. Patients will be consecutively recruited within 24 hours of emergency presentation and followed-up until 90 days from hospital admission. We will conduct enhanced diagnostic tests with robust quality assurance and quality control to determine estimates of disease pathology. Diagnostic case definitions were selected following a systematic literature search. Discussion This study will provide detailed epidemiological description of adult hospital admissions due to breathlessness in low-income settings, which is currently poorly understood. We will delineate between causes using established case definitions and conduct nested diagnostic evaluation. The results have the potential to facilitate development of interventions targeted to strengthen diagnostic capacity, enable prompt and appropriate treatment, and ultimately improve both patient care and outcomes.

Following sensory deprivation, areas and networks in the brain may adapt and reorganize to compensate for the loss of input. These adaptations are manifestations of compensatory crossmodal plasticity, which has been documented in both human and animal models of deafness–including the domestic cat. Although there are abundant examples of structural plasticity in deaf felines from retrograde tracer-based studies, there is a lack of diffusion-based knowledge involving this model compared to the current breadth of human research. The purpose of this study was to explore white matter structural adaptations in the perinatally-deafened cat via tractography, increasing the methodological overlap between species. Plasticity was examined by identifying unique group connections and assessing altered connectional strength throughout the entirety of the brain. Results revealed a largely preserved connectome containing a limited number of group-specific or altered connections focused within and between sensory networks, which is generally corroborated by deaf feline anatomical tracer literature. Furthermore, five hubs of cortical plasticity and altered communication following perinatal deafness were observed. The limited differences found in the present study suggest that deafness-induced crossmodal plasticity is largely built upon intrinsic structural connections, with limited remodeling of underlying white matter.

Introduction Since the introduction of pneumococcal conjugate vaccines, pneumococcal disease rates have declined for many vaccine-type serotypes. However, serotype 3 (SPN3) continues to cause significant disease and is identified in colonisation epidemiological studies as one of the top circulating serotypes in adults in the UK. Consequently, new vaccines that provide greater protection against SPN3 colonisation/carriage are urgently needed. The Experimental Human Pneumococcal Challenge (EHPC) model is a unique method of determining pneumococcal colonisation rates, understanding acquired immunity, and testing vaccines in a cost-effective manner. To enhance the development of effective pneumococcal vaccines against SPN3, we aim to develop a new relevant and safe SPN3 EHPC model with high attack rates which could be used to test vaccines using small sample size.Methods and analysis This is a human challenge study to establish a new SPN3 EHPC model, consisting of two parts. In the dose-ranging/safety study, cohorts of 10 healthy participants will be challenged with escalating doses of SPN3. If first challenge does not lead into colonisation, participants will receive a second challenge 2 weeks after. Experimental nasopharyngeal (NP) colonisation will be determined using nasal wash sampling. Using the dose that results in ≥50% of participants being colonised, with a high safety profile, we will complete the cohort with another 33 participants to check for reproducibility of the colonisation rate. The primary outcome of this study is to determine the optimal SPN3 dose and inoculation regime to establish the highest rates of NP colonisation in healthy adults. Secondary outcomes include determining density and duration of experimental SPN3 NP colonisation and characterising mucosal and systemic immune responses to SPN3 challenge.Ethics and dissemination This study is approved by the NHS Research and Ethics Committee (reference 22/NW/0051). Findings will be published in peer-reviewed journals and reports will be made available to participants.

Background: As well as suffering a high burden of pneumococcal disease people living with HIV (PLHIV) may contribute to community transmission in sub-Saharan African (sSA) settings. Pneumococcal vaccination is not currently offered to PLHIV in sSA but may prevent disease and reduce transmission. More evidence of vaccine effectiveness against carriage in PLHIV is needed. An Experimental Human Pneumococcal Carriage model (EHPC) has been safely and acceptably used in healthy adults in Malawi to evaluate pneumococcal vaccines against carriage and to identify immune correlates of protection from carriage. This study will establish the same model in PLHIV and will be the first controlled human infection model (CHIM) in this key population. Methods: Healthy participants with and without HIV will be inoculated intranasally with Streptococcus pneumoniae serotype 6B. Sequential cohorts will be challenged with increasing doses to determine the optimal safe challenge dose to establish experimental carriage. Nasal fluid, nasal mucosal, and blood samples will be taken before inoculation and on days 2, 7, 14, and 21 following inoculation to measure pneumococcal carriage density and identify immune correlates of protection from carriage. The vast majority of natural pneumococcal carriage events in PLHIV do not result in invasive disease and no invasive disease is expected in this study. However, robust participant safety monitoring is designed to identify signs of invasive disease early should they develop, and to implement treatment immediately. Participants will complete a Likert-style questionnaire at study-end to establish acceptability. Interpretations: We expect the EHPC model to be safely and acceptably implemented in PLHIV. The CHIM can then be used to accelerate pneumococcal vaccine evaluations in this population, and an evidence-based pneumococcal vaccination policy for PLHIV in sSA.

Abstract Background Binding and neutralising anti-Spike antibodies play a key role in immune defence against SARS-CoV-2 infection. Since it is known that antibodies wane with time and new immune-evasive variants are emerging, we aimed to assess the dynamics of anti-Spike antibodies in an African adult population with prior SARS-CoV-2 infection and to determine the effect of subsequent COVID-19 vaccination. Methods Using a prospective cohort design, we recruited adults with prior laboratory-confirmed mild/moderate COVID-19 in Blantyre, Malawi, and followed them up for 270 days (n = 52). A subset of whom subsequently received a single dose of the AstraZeneca COVID-19 vaccine (ChAdOx nCov-19) (n = 12). We measured the serum concentrations of anti-Spike and receptor-binding domain (RBD) IgG antibodies using a Luminex-based assay. Anti-RBD antibody cross-reactivity across SARS-CoV-2 variants of concern (VOC) was measured using a haemagglutination test. A pseudovirus neutralisation assay was used to measure neutralisation titres across VOCs. Ordinary or repeated measures one-way ANOVA was used to compare log10 transformed data, with p value adjusted for multiple comparison using Šídák's or Holm-Šídák's test. Results We show that neutralising antibodies wane within 6 months post mild/moderate SARS-CoV-2 infection (30–60 days vs. 210–270 days; Log ID50 6.8 vs. 5.3, p = 0.0093). High levels of binding anti-Spike or anti-RBD antibodies in convalescent serum were associated with potent neutralisation activity against the homologous infecting strain (p

Abstract Previous studies have suggested that the pneumococcal niche changes from the nasopharynx to the oral cavity with age. We use an Experimental Human Pneumococcal Challenge model to investigate pneumococcal colonisation in different anatomical niches with age. Healthy adults (n = 112) were intranasally inoculated with Streptococcus pneumoniae serotype 6B (Spn6B) and were categorised as young 18–55 years (n = 57) or older > 55 years (n = 55). Colonisation status (frequency and density) was determined by multiplex qPCR targeting the lytA and cpsA-6A/B genes in both raw and culture-enriched nasal wash and oropharyngeal swab samples collected at 2-, 7- and 14-days post-exposure. For older adults, raw and culture-enriched saliva samples were also assessed. 64% of NW samples and 54% of OPS samples were positive for Spn6B in young adults, compared to 35% of NW samples, 24% of OPS samples and 6% of saliva samples in older adults. Many colonisation events were only detected in culture-enriched samples. Experimental colonisation was detected in 72% of young adults by NW and 63% by OPS. In older adults, this was 51% by NW, 36% by OPS and 9% by saliva. The nose, as assessed by nasal wash, is the best niche for detection of experimental pneumococcal colonisation in both young and older adults.

Abstract A role for vitamin D in the immune system is emerging from human research but data in the bovine is limited. In the current study, 48 Holstein–Friesian calves were randomly assigned to one of 4 groups designed to expose calves to divergent vitamin D levels for a 7 month period and to determine its effects on circulating immunity in young calves. Concentrations of circulating 25-hydroxyvitamin D (25OHD) was measured in serum using a commercial ELISA with validated bovine standards. Results showed that mean circulating concentrations of 25OHD at birth was 7.64 ± 3.21 ng/ml indicating vitamin D deficiency. Neither the injection of Vit D3 at birth nor the elevated levels in milk replacer yield discernible changes to pre-weaning circulating concentration of 25OHD. No calf reached the recommended level of vitamin D immune sufficiencyof 30 ng/ml of 25OHD until at least 3 months of age (T4). Increasing dietary Vit D3 via ration in the post-weaning period significantly elevated 25OHD concentrations in serum in VitD-In calves. Maximal levels of circulating 25OHD were achieved in VitD-Out calves, reaching 60.86 ± 7.32 ng/ml at 5 months of age (T7). Greatest divergence in haematology profile was observed between Ctl-In vs VitD-In groups with Ctl-In calves showing an elevated count of neutrophils, eosinophils, and basophils associated with reduced 25OHD concentrations. Neither IL-8 expression nor ROS production in serum were significantly different between calves with high and low 25OHD, indicating that other vitamin D-dependent mechanisms may contribute to the divergent circulating cellular profiles observed. This novel data on the vitamin D status of neonatal calves identifies a significant window of vitamin D insufficiency which is associated with significant differences in circulating immune cell profiles. Vitamin D insufficiency may therefore exacerbate pre-weaning disease susceptibility, and further work in now warranted.

Clinical management of COVID-19 in resource-poor settings has distinct challenges and detailed patient characterisation is needed. Here, the authors describe the clinical and immunological profiles of patients at a hospital in Malawi with confirmed and suspected COVID-19.

Introduction Despite widely available vaccinations, Streptococcus pneumoniae (SPN) remains a major cause of morbidity and mortality worldwide, causing community-acquired pneumonia, meningitis, otitis media, sinusitis and bacteraemia. Here, we summarise an ethically approved protocol for a double-blind, randomised controlled trial investigating the effect of the 13-valent pneumococcal conjugate vaccine (PCV13) and the 23-valent pneumococcal polysaccharide vaccine (PPV23) on pneumococcal nasopharyngeal colonisation acquisition, density and duration using experimental human pneumococcal challenge (EHPC).Methods and analysis Healthy adult participants aged 18–50 years will be randomised to receive PCV13, PPV23 or placebo and then undergo one or two EHPCs involving intranasal administration of SPN at 1-month post-vaccination with serotype 3 (SPN3) and 6 months with serotype 6B (SPN6B). Participants randomised to PCV13 and placebo will also be randomised to one of two clinically relevant SPN3 strains from distinct lineages within clonal complex 180, clades Ia and II, creating five study groups. Following inoculation, participants will be seen on days 2, 7, 14 and 23. During the follow-up period, we will monitor safety, colonisation status, density and duration, immune responses and antigenuria. The primary outcome of the study is comparing the rate of SPN3 acquisition between the vaccinated (PCV13 or PPV23) and unvaccinated (placebo) groups as defined by classical culture. Density and duration of colonisation, comparison of acquisition rates using molecular methods and evaluation of the above measurements for individual SPN3 clades and SPN6B form the secondary objectives. Furthermore, we will explore the immune responses associated with these vaccines, their effect on colonisation and the relationship between colonisation and urinary pneumococcal antigen detection.Ethics and dissemination The study is approved by the NHS Research and Ethics Committee (Reference: 20/NW/0097) and by the Medicines and Healthcare products Regulatory Agency (Reference: CTA 25753/0001/001–0001). Findings will be published in peer-reviewed journals.Trial registration number ISRCTN15728847, NCT04974294.

Streptococcus pneumoniae is the leading cause of morbidity and mortality due to community acquired pneumonia, bacterial meningitis and bacteraemia worldwide. Pneumococcal conjugate vaccines protect against invasive disease, but are expensive to manufacture, limited in serotype coverage, associated with serotype replacement, and demonstrate reduced effectiveness against mucosal colonisation. For Malawi, nasopharyngeal carriage of vaccine-type pneumococci is common in vaccinated children despite national roll-out of 13-valent pneumococcal conjugate vaccine (PCV13) since 2011. Our team has safely transferred an established experimental human pneumococcal carriage method from Liverpool School of Tropical Medicine to the Malawi-Liverpool Wellcome Trust Clinical Research Programme, Malawi. This study will determine potential immunological mechanisms for the differential effects of PCV13 on nasal carriage between healthy Malawian and UK populations. We will conduct a double-blinded randomised controlled trial to vaccinate (1:1) participants with either PCV13 or control (normal saline). After a period of one month, participants will be inoculated with S. pneumoniae serotype 6B to experimentally induce nasal carriage using the EHPC method. Subsequently, participants will be invited for a second inoculation after one year to determine longer-term vaccine-induced immunological effects. Primary endpoint: detection of inoculated pneumococci by classical culture from nasal wash recovered from the participants after pneumococcal challenge. Secondary endpoints: local and systemic innate, humoral and cellular responses to PCV-13 with and without pneumococcal nasal carriage The primary objective of this controlled human infection model study is to determine if PCV-13 vaccination is protective against pneumococcal carriage in healthy adult Malawian volunteers. This study will help us to understand the observed differences in PCV-13 efficacy between populations and inform the design of future vaccines relevant to the Malawian population. Trial Registration: Pan African Clinical Trial Registry (REF: PACTR202008503507113)

The Mycobacterium tuberculosis complex (MTBC) contains the causative agents of tuberculosis (TB) in mammals. The archetypal members of the MTBC, Mycobacterium tuberculosis and Mycobacterium bovis, cause human tuberculosis and bovine tuberculosis, respectively. Although M. tuberculosis and M. bovis share over 99.9% genome identity, they show distinct host adaptation for humans and animals; hence, while the molecular basis of host adaptation is encoded in their genomes, the mechanistic basis of host tropism is still unclear. Exploration of the in vitro phenotypic consequences of known genetic difference between M. bovis and M. tuberculosis offers one route to explore genotype–phenotype links that may play a role in host adaptation. The TbD1 (“Mycobacterium tuberculosis deletion 1 region”) locus encompasses the mmpS6 and mmpL6 genes. TbD1 is absent in M. tuberculosis “modern” lineages (Lineages 2, 3, and 4) but present in “ancestral” M. tuberculosis (Lineages 1 and 7), Mycobacterium africanum lineages (Lineages 5 and 6), newly identified M. tuberculosis lineages (Lineages 8 and 9), and animal adapted strains, such as M. bovis. The function of TbD1 has previously been investigated in M. tuberculosis, where conflicting data has emerged on the role of TbD1 in sensitivity to oxidative stress, while the underlying mechanistic basis of such a phenotype is unclear. In this study, we aimed to shed further light on the role of the TbD1 locus by exploring its function in M. bovis. Toward this, we constructed an M. bovis TbD1 knockout (ΔTbD1) strain and conducted comparative transcriptomics to define global gene expression profiles of M. bovis wild-type (WT) and the ΔTbD1 strains under in vitro culture conditions (rolling and standing cultures). This analysis revealed differential induction of a hypoxia-driven copper response in WT and ΔTbD1 strains. In vitro phenotypic assays demonstrated that the deletion of TbD1 sensitized M. bovis to H2O2 and hypoxia-specific copper toxicity. Our study provides new information on the function of the TbD1 locus in M. bovis and its role in stress responses in the MTBC.

This study investigated the survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in sandy and clay loam textured soils when applied in bovine slurry or unpasteurised digestate, using laboratory based inoculation studies. The run-off rate for a test bacterium, Listeria innocua, when applied to grass in slurry and digestate, was also examined using field studies. Bovine slurry and digestate were inoculated with the target bacteria to a final concentration of 106 log10 cfu/g or spores/g, thoroughly mixed into soil samples and incubated at 4°C or 14°C. Samples were removed periodically and the surviving cells enumerated using AOAC or equivalent methods. The loss of viability/culturability phase followed first order kinetics and T90 values ranged from 11.9 to 166.7 d at 4°C and from 6.0 to 156 d at 14°C. With the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C (T90 values were significantly (P < 0.05) higher in slurry) the type of soil texture or application material (slurry or digestate) did not affect survival rates. In the field study, 12 grass covered micro-plots were prepared. L. innocua was applied in digestate and bovine slurry and rainfall was simulated at a target rate of ~11 mm per plot per h−1. Rainfall simulation (30 min) took place after 24, 48 h, 14 d and 30 d. Run-off samples were tested for the L. innocua strain using Brilliance Listeria agar supplemented with streptomycin sulphate (1,000 μg/ml) at 37°C for 48 h, as were soil samples after 30, 58, 86 and 112 d. Significantly (P < 0.05) lower counts were obtained in the run-off from digestate after 1, 2 and 30 d as compared to slurry. It was concluded that the type of organic fertiliser does not affect the bacterial survival rates in sandy and clay soils, with the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C. Furthermore, bacteria may be retained better in the soil-digestate matrices during rainfall although additional research is required to further validate and provide the scientific basis for this observation.

This paper examines the behavioural factors influencing investment decisions and strategy in the Sultanate of Oman. Investors’ decision-making process is thought to be influenced by a wide range of factors directly or indirectly (Kusev et al. 2017). The rational approach considers only the mathematical results thereby failing to recognize the investor’s related psychological and sociological factors, categorized in the paper as heuristic factors, prospect factors and herding factors. This study attempts to identify the behavioural factors that influence individual investors’ decision in the Muscat Securities Market (MSM). Specifically, the study was designed to identify the factors which are mostly influencing the investment decisions of investors. Employing descriptive research design; data were collected from individual investors who had traded in the MSM during the fourth quarter of 2018. The primary collected through structured questionnaire and the secondary data is collected from various sources from stock brokers, Journals and other sources respectively. The simple random sampling technique was applied and the collected data covering 16 variables of behavioural factors were analyzed using the factor analysis, principal component analysis with varimax rotation, and Analysis of Variance tools. The anchoring, mental accounting, movement of prices, volume of trade and market information factors emerged as the five principal determinants of investment strategy are the major findings of the study. The results might make investors and advisors to understand the optimal ways to improve on strategy for structuring optimum portfolio selection and how far this can be optimised further in terms of managing their investment behaviour.

Summary: Background: Inclusive universal health coverage requires access to quality health care without financial barriers. Receipt of palliative care after advanced cancer diagnosis might reduce household poverty, but evidence from low-income and middle-income settings is sparse. Methods: In this prospective study, the primary objective was to investigate total household costs of cancer-related health care after a diagnosis of advanced cancer, with and without the receipt of palliative care. Households comprising patients and their unpaid family caregiver were recruited into a cohort study at Queen Elizabeth Central Hospital in Malawi, between Jan 16 and July 31, 2019. Costs of cancer-related health-care use (including palliative care) and health-related quality-of-life were recorded over 6 months. Regression analysis explored associations between receipt of palliative care and total household costs on health care as a proportion of household income. Catastrophic costs, defined as 20% or more of total household income, sale of assets and loans taken out (dissaving), and their association with palliative care were computed. Findings: We recruited 150 households. At 6 months, data from 89 (59%) of 150 households were available, comprising 89 patients (median age 50 years, 79% female) and 64 caregivers (median age 40 years, 73% female). Patients in 55 (37%) of the 150 households died and six (4%) were lost to follow-up. 19 (21%) of 89 households received palliative care. Catastrophic costs were experienced by nine (47%) of 19 households who received palliative care versus 48 (69%) of 70 households who did not (relative risk 0·69, 95% CI 0·42 to 1·14, p=0·109). Palliative care was associated with substantially reduced dissaving (median US$11, IQR 0 to 30 vs $34, 14 to 75; p=0·005). The mean difference in total household costs on cancer-related health care with receipt of palliative care was −36% (95% CI −94 to 594; p=0·707). Interpretation: Vulnerable households in low-income countries are subject to catastrophic health-related costs following a diagnosis of advanced cancer. Palliative care might result in reduced dissaving in these households. Further consideration of the economic benefits of palliative care is justified. Funding: Wellcome Trust; National Institute for Health Research; and EMMS International.

Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.

Pupil size is influenced by cognitive and non-cognitive factors. One of the strongest modulators of pupil size is scene luminance, which complicates studies of cognitive pupillometry in environments with complex patterns of visual stimulation. To help understand how dynamic visual scene statistics influence pupil size during an active visual search task in a visually rich 3D virtual environment (VE), we analyzed the correlation between pupil size and intensity changes of image pixels in the red, green, and blue (RGB) channels within a large window (~14 degrees) surrounding the gaze position over time. Overall, blue and green channels had a stronger influence on pupil size than the red channel. The correlation maps were not consistent with the hypothesis of a foveal bias for luminance, instead revealing a significant contextual effect, whereby pixels above the gaze point in the green/blue channels had a disproportionate impact on pupil size. We hypothesized this differential sensitivity of pupil responsiveness to blue light from above as a “blue sky effect,” and confirmed this finding with a follow-on experiment with a controlled laboratory task. Pupillary constrictions were significantly stronger when blue was presented above fixation (paired with luminance-matched gray on bottom) compared to below fixation. This effect was specific for the blue color channel and this stimulus orientation. These results highlight the differential sensitivity of pupillary responses to scene statistics in studies or applications that involve complex visual environments and suggest blue light as a predominant factor influencing pupil size.

Background: Persistent carriage of pneumococcal vaccine serotypes has occurred after introduction of PCV13 vaccination in Africa but the mechanisms are unclear. We tested the feasibility of using a human pneumococcal challenge model in Malawi to understand immune correlates of protection against carriage and to trial alternative vaccine candidates. We aimed to identify a dose of Streptococcus pneumoniae serotype 6B sufficient to establish nasopharyngeal carriage in 40% of those nasally inoculated and evaluate nasal mucosal immunity before and after experimental inoculation. Methods: Healthy student volunteers were recruited and inoculated with saline, 20,000 CFU/naris or 80,000 CFU/naris of Streptococcus pneumoniae serotype 6B Post inoculation carriage was determined by nasal sampling for bacterial culture and lytA PCR. Immunological responses were measured in serum and nasal mucosal biopsies before and after bacterial inoculation. Findings: Twenty-four subjects completed the feasibility protocol with minimal side effects. pneumococcal carriage was established in 0/6, 3/9 and 4/9 subjects in the saline, 20,000 CFU/naris and 80,000 CFU/naris groups, respectively. Incidental (natural) serotype carriage was common (7/24 participants carried non-6B strains, 29.2%. Experimentally induced type 6B pneumococcal carriage was associated with pro-inflammatory nasal mucosal responses prior to inoculation and altered mucosal recruitment of immune cells post bacterial challenge. There was no association with serum anti-capsular antibody. Interpretation: The serotype 6B experimental human pneumococcal carriage model is feasible in Malawi and can now be used to determine the immunological correlates of protection against carriage and vaccine efficacy in this population. Funding: None.

Objective: Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. Methods: DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. Results: The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n = 2/8) and SIT3234 (n = 8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 (n = 19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. Conclusions: The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring. Keywords: Mycobacterium tuberculosis, Spoligotype, MIRU-VNTR, Lineage 4 (Euro-American lineage), Sri Lanka

Occurrence of lower respiratory tract infections requires prior colonization of the upper respiratory tract with a pathogen. Most bacterial infection and colonization studies have been performed in murine and in vitro

Species belonging to the Mycobacterium tuberculosis Complex (MTBC) show more than 99% genetic identity but exhibit distinct host preference and virulence. The molecular genetic changes that underly host specificity and infection phenotype within MTBC members have not been fully elucidated. Here, we analysed RD900 genomic region across MTBC members using whole genome sequences from 60 different MTBC strains so as to determine its role in the context of MTBC evolutionary history. The RD900 region comprises two homologous genes, pknH1 and pknH2, encoding a serine/threonine protein kinase PknH flanking the tbd2 gene. Our analysis revealed that RD900 has been independently lost in different MTBC lineages and different strains, resulting in the generation of a single pknH gene. Importantly, all the analysed M. bovis and M. caprae strains carry a conserved deletion within a proline rich-region of pknH, independent of the presence or absence of RD900. We hypothesized that deletion of pknH proline rich-region in M. bovis may affect PknH function, having a potential role in its virulence and evolutionary adaptation. To explore this hypothesis, we constructed two M. bovis 'knock-in' strains containing the M. tuberculosis pknH gene. Evaluation of their virulence phenotype in mice revealed a reduced virulence of both M. bovis knock-in strains compared to the wild type, suggesting that PknH plays an important role in the differential virulence phenotype of M. bovis vs M. tuberculosis.

Academic global pulmonary/critical care medicine (PCCM) remains a relatively novel concept not fully embraced by all training programs, so PCCM early-career professionals may have little guidance in building successful careers in this field. To highlight various approaches used by current PCCM faculty to incorporate global health into their academic careers, speakers from a global health careers mini symposia held at the 2017 and 2018 American Thoracic Society International Conferences were invited to submit perspectives reflecting on academic PCCM and global health. The collection of essays was collated into a single manuscript. Eight current global PCCM faculty from diverse geographic and professional backgrounds provide experiential guidance for early-career professionals interested in global academic PCCM. Trainees and junior faculty interested in academic global PCCM will find innumerable obstacles to developing this non-traditional career pathway, but there exist diverse pathways to success.

Background: Many households in low-and-middle income countries face the additional burden of crippling out-of-pocket expenditure when faced with a diagnosis of life-limiting illness. Available evidence suggests that receipt of palliative care supports cost-savings for cancer-affected households. This study will explore the relationship between receipt of palliative care, total household out-of-pocket expenditure on health and wellbeing following a first-time diagnosis of advanced cancer at Queen Elizabeth Central Hospital in Blantyre, Malawi. Protocol: Patients and their primary family caregivers will be recruited at the time of cancer diagnosis. Data on healthcare utilisation, related costs, coping strategies and wellbeing will be gathered using new and existing questionnaires (the Patient-and-Carer Cancer Cost Survey, EQ-5D-3L and the Integrated Palliative Care Outcome Score). Surveys will be repeated at one, three and six months after diagnosis. In the event of the patient’s death, a brief five-item questionnaire on funeral costs will be administered to caregivers not less than two weeks following the date of death. Descriptive and Poisson regression analyses will assess the relationship between exposure to palliative care and total household expenditure from baseline to six months. A sample size of 138 households has been calculated in order to detect a medium effect (as determined by Cohen’s f 2=0.15) of receipt of palliative care in a regression model for change in total household out-of-pocket expenditure as a proportion of annual household income. Ethics and dissemination: The study has received ethical approval. Results will be reported using STROBE guidelines and disseminated through scientific meetings, open access publications and a national stakeholder meeting. Conclusions: This study will provide data on expenditure for healthcare by households affected by advanced cancer in Malawi. We also explore whether receipt of palliative care is associated with a reduction in out-of-pocket expenditure at household level.

Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (Pol II) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density genome-wide association study (GWAS) data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and Pol II at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.

Summary: Increased glycolytic metabolism recently emerged as an essential process driving host defense against Mycobacterium tuberculosis (Mtb), but little is known about how this process is regulated during infection. Here, we observe repression of host glycolysis in Mtb-infected macrophages, which is dependent on sustained upregulation of anti-inflammatory microRNA-21 (miR-21) by proliferating mycobacteria. The dampening of glycolysis by miR-21 is mediated through targeting of phosphofructokinase muscle (PFK-M) isoform at the committed step of glycolysis, which facilitates bacterial growth by limiting pro-inflammatory mediators, chiefly interleukin-1β (IL-1β). Unlike other glycolytic genes, PFK-M expression and activity is repressed during Mtb infection through miR-21-mediated regulation, while other less-active isoenzymes dominate. Notably, interferon-γ (IFN-γ), which drives Mtb host defense, inhibits miR-21 expression, forcing an isoenzyme switch in the PFK complex, augmenting PFK-M expression and macrophage glycolysis. These findings place the targeting of PFK-M by miR-21 as a key node controlling macrophage immunometabolic function. : Hackett et al. identify a role for the anti-inflammatory miR-21 in limiting host glycolysis during tuberculosis (TB) infection to favor bacterial replication. This occurs by targeting a pro-glycolytic isoform at the rate-limiting step in glycolysis, PFK-M, a process antagonized by the host Th1-cytokine IFN-γ, to promote full macrophage activation and antimicrobial function. Keywords: macrophage, metabolic reprogramming, tuberculosis, mycobacterium tuberculosis, glycolysis, microRNA, miR-21, interleukin-1b, phosphofructokinase, interferon gamma

Background: Many households in low-and-middle income countries face the additional burden of crippling out-of-pocket expenditure when faced with a diagnosis of life-limiting illness. Available evidence suggests that receipt of palliative care supports cost-savings for cancer-affected households. This study will explore the relationship between receipt of palliative care, total household out-of-pocket expenditure on health and wellbeing following a first-time diagnosis of advanced cancer at Queen Elizabeth Central Hospital in Blantyre, Malawi. Protocol: Patients and their primary family caregivers will be recruited at the time of cancer diagnosis. Data on healthcare utilisation, related costs, coping strategies and wellbeing will be gathered using new and existing questionnaires (the Patient-and-Carer Cancer Cost Survey, EQ-5D-3L and the Integrated Palliative Care Outcome Score). Surveys will be repeated at one, three and six months after diagnosis. In the event of the patient’s death, a brief five-item questionnaire on funeral costs will be administered to caregivers not less than two weeks following the date of death. Descriptive and Poisson regression analyses will assess the relationship between exposure to palliative care and total household expenditure from baseline to six months. A sample size of 138 households has been calculated in order to detect a medium effect (as determined by Cohen’s f2=0.15) of receipt of palliative care in a regression model for change in total household out-of-pocket expenditure as a proportion of annual household income. Ethics and dissemination: The study has received ethical approval. Results will be reported using STROBE guidelines and disseminated through scientific meetings, open access publications and a national stakeholder meeting. Conclusions: This study will provide data on expenditure for healthcare by households affected by cancer in Malawi. We also explore whether receipt of palliative care is associated with a reduction in out-of-pocket expenditure at household level.

IntroductionPneumococcal colonisation is regarded as a pre-requisite for developing pneumococcal disease. In children previous studies have reported pneumococcal colonisation to be a symptomatic event and described a relationship between symptom severity/frequency and colonisation density. The evidence for this in adults is lacking in the literature. This study uses the experimental human pneumococcal challenge (EHPC) model to explore whether pneumococcal colonisation is a symptomatic event in healthy adults.MethodsHealthy participants aged 18-50 were recruited and inoculated intra-nasally with either Streptococcus pneumoniae (serotypes 6B, 23F) or saline as a control. Respiratory viral swabs were obtained prior to inoculation. Nasal and non-nasal symptoms were then assessed using a modified Likert score between 1 (no symptoms) to 7 (cannot function). The rate of symptoms reported between the two groups was compared and a correlation analysis performed.ResultsData from 54 participants were analysed. 46 were inoculated with S. pneumoniae (29 with serotype 6B, 17 with serotype 23F) and 8 received saline (control). In total, 14 became experimentally colonised (30.4%), all of which were inoculated with serotype 6B. There was no statistically significant difference in nasal (p = 0.45) or non-nasal symptoms (p = 0.28) between the inoculation group and the control group. In those who were colonised there was no direct correlation between colonisation density and symptom severity. In the 22% (12/52) who were co-colonised, with pneumococcus and respiratory viruses, there was no statistical difference in either nasal or non-nasal symptoms (virus positive p = 0.74 and virus negative p = 1.0).ConclusionPneumococcal colonisation using the EHPC model is asymptomatic in healthy adults, regardless of pneumococcal density or viral co-colonisation.

Objectives: Myanmar is a World Health Organization high tuberculosis (TB) burden country with a high multidrug-resistant (MDR)-TB burden. Of significance, a high prevalence of the Beijing genotype of Mycobacterium tuberculosis (MTB) among MDR-MTB has been reported previously. A detailed genetic characterization of TB clinical isolates was performed in order to explore whether there is an association between the prevalence of the Beijing MTB genotype and MDR-TB in Myanmar. Methods: A total of 265 MDR-MTB clinical isolates collected in 2010 and 2012 were subjected to spoligotyping, mycobacterial interspersed repetitive unit–variable number tandem repeat (MIRU-VNTR) analysis, single nucleotide polymorphism (SNP) typing, and drug resistance-associated gene sequencing, including rpoC to detect potential compensatory evolution. Results: Of the total MDR-MTB isolates, 79.2% (210/265) were of the Beijing genotype, the majority of which were the ‘modern’ subtype. Beijing genotype isolates were differentiated by 15-locus MIRU-VNTR and a high clustering rate (53.0%) was observed in the modern subtype. These MIRU-VNTR patterns were similar to Beijing genotype clones spreading across Russia and Central Asia. A high prevalence of katG Ser315Thr, and genetic evidence of extensive drug resistance (XDR) and pre-XDR and compensatory mutations in rpoC were observed among clustered isolates. Conclusions: MDR-MTB strains of the Beijing genotype might be spreading in Myanmar and present a major challenge to TB control in this country. Keywords: Mycobacterium tuberculosis, Multidrug-resistant TB, Beijing genotype, MIRU-VNTR, Myanmar

Abstract Background The incidence of community-acquired pneumonia and lower respiratory tract infection rises considerably in later life. Immunoglobulin M (IgM) antibody levels to pneumococcal capsular polysaccharide are known to decrease with age; however, whether levels of IgM antibody to pneumococcal proteins are subject to the same decline has not yet been investigated. Methods This study measured serum levels and binding capacity of IgM antibody specific to the pneumococcal surface protein A (PspA) and an unencapsulated pneumococcal strain in serum isolated from hospital patients aged

Abstract Background Broncho alveolar lavage (BAL) is widely used for investigative research to study innate, cellular and humoral immune responses, and in early phase drug trials. Conventional (multiple use) flexible bronchoscopes have time and monetary costs associated with cleaning, and carries a small risk of cross infection. Single use bronchoscopes may provide an alternative, but have not been evaluated in this context. Methods Healthy volunteers underwent bronchoscopy at a day-case clinical research unit using the Ambu® aScopeTM single-use flexible intubation bronchoscope. Broncho alveolar lavage was performed from a sub segmental bronchus within the right middle lobe; a total of 200 ml of warmed normal saline was instilled then aspirated using handheld suction. BAL volume yield, cell yield and viability were recorded. Results Ten volunteers, (mean age 23 years, six male) participated. Bronchoscopies were carried out by one of two senior bronchoscopists, experienced in the technique of obtaining BAL for research purposes. The results were compared to 50 (mean age 23, 14 male) procedures performed using the conventional scope by the same two bronchoscopists. The total volume yield was significantly higher in the disposable group median 152 ml (IQR 141–166 ml) as compared to conventional 124 ml (110–135 ml), p =

Abstract Background In urban settings of Africa with rapidly increasing population, traffic-related air pollution is a major contributor to outdoor air pollution (OAP). Although OAP has been identified as a leading cause of global morbidity and mortality, there is however, lack of a simple biomarker to assess levels of exposure to OAP in resource-poor settings. This study evaluated the role of exhaled carbon monoxide (exhCO) as a potential biomarker of exposure to ambient carbon monoxide (ambCO) from OAP. Methods This was a descriptive study conducted among male commercial motorcycle riders in Cotonou – the economic capital of Benin. The participants’ AmbCO was measured using a portable carbon monoxide (CO) data logger for 8 h during the period of their shift. ExhCO was measured just before and immediately after their shift (8-h) Participants were asked not to cook or to smoke during the day of the measurements. Linear regression analysis was used to assess the association between ambCO and exhCO for the last 2, 4 and 6 h of their shift. Results Of 170 participants who completed the study, their mean ± SD age was 42.2 ± 8.4 years, and their mean ± SD daily income was 7.3 ± 2.7$. Also, 95% of the participants’ used solid fuels for cooking and only 2% had ever smoked. Average exhCO increased by 5.1 ppm at the end of the shift (p = 0.004). Post-shift exhCO was significantly associated to ambCO, this association was strongest for the last 2 h of OAP exposure before exhCO measurement (β = 0.34, p

Deep convolutional neural networks (CNN) have previously been shown to be useful tools for signal decoding and analysis in a variety of complex domains, such as image processing and speech recognition. By learning from large amounts of data, the representations encoded by these deep networks are often invariant to moderate changes in the underlying feature spaces. Recently, we proposed a CNN architecture that could be applied to electroencephalogram (EEG) decoding and analysis. In this article, we train our CNN model using data from prior experiments in order to later decode the P300 evoked response from an unseen, hold-out experiment. We analyze the CNN output as a function of the underlying variability in the P300 response and demonstrate that the CNN output is sensitive to the experiment-induced changes in the neural response. We then assess the utility of our approach as a means of improving the overall signal-to-noise ratio in the EEG record. Finally, we show an example of how CNN-based decoding can be applied to the analysis of complex data.

Although community engagement is increasingly promoted in global health research to improve ethical research practice, there is sometimes a disconnect between the broader moral ambitions for community engagement in the literature and guidelines on the one hand and its rather narrower practical application in health research on the other. In practice, less attention is paid to engaging communities for the ‘intrinsic’ value of showing respect and ensuring inclusive participation of community partners in research design. Rather, more attention is paid to the use of community engagement for ‘instrumental’ purposes to improve community understanding of research and ensure successful study implementation. Against this backdrop, we reviewed the literature and engaged various research stakeholders at a workshop to discuss ways of strengthening ethical engagement of communities and to develop context-relevant guidelines for community engagement in health research in Malawi.

Background: Research participant remuneration has been variable and inconsistent world-wide for many years owing to uncertainty regarding best practice and a lack of written guidelines for investigators and research ethics committees. Recent recommendations are that researchers and regulators should develop regionally appropriate written guidelines to define reasonable remuneration based on expense reimbursement, compensation for time and burden associated with participation. Incentives to motivate participation are acceptable in specific circumstances. Methods: We wished to develop regionally informed, precise and applicable guidelines in Malawi that might also be generally useful for African researchers and review committees. We therefore reviewed the current literature and developed widely applicable and specific remuneration tables using acceptable and evidence-based payment rationales. Results: There were good international guidelines and limited published regional guidelines. There were published examples of best practice and sufficient material to suggest a structured remuneration table. The rationale and method for the table were discussed at an inter-disciplinary workshop resulting in a reimbursement and compensation model with fixed rates. Payment is recommended pro rata and equally across a study. Conclusions: Transparent, fair remuneration of research participants is recommended by researchers and regulators in Malawi. The means to achieve this are now presented in the Malawi research participant remuneration table.

Rationale: Nasopharyngeal administration of live virulence-attenuated Streptococcus pneumoniae strains is a potential novel preventative strategy. One target for creating reduced virulence S. pneumoniae strains is the capsule, but loss of the capsule reduces the duration of S. pneumoniae colonisation in mice which could impair protective efficacy against subsequent infection. Objectives: To assess protective efficacy of nasopharyngeal administration of unencapsulated S. pneumoniae strains in murine infection models. Methods: Strains containing cps locus deletions combined with the S. pneumoniae virulence factors psaA (reduces colonisation) or proABC (no effect on colonisation) were constructed and their virulence phenotypes and ability to prevent recolonisation or invasive infection assessed using mouse infection models. Serological responses to colonisation were compared between strains using ELISAs, immunoblots and 254 S. pneumoniae protein antigen array. Measurements and Main Results: The ∆cps/piaA and ∆cps/proABC strains were strongly attenuated in virulence in both invasive infection models and had a reduced ability to colonise the nasopharynx. ELISAs, immunoblots and protein arrays showed colonisation with either strain stimulated weaker serological responses than the wild type strain. Mice previously colonised with these strains were protected against septicaemic pneumonia but, unlike mice colonised with the wild type strain, not against S. pneumoniae recolonisation. Conclusions: Colonisation with the ∆cps/piaA and ∆cps/proABC strains prevented subsequent septicaemia, but in contrast, to published data for encapsulated double mutant strains they did not prevent recolonisation with S. pneumoniae. These data suggest targeting the cps locus is a less effective option for creating live attenuated strains that prevent S. pneumoniae infections.

Although community engagement is increasingly promoted in global health research to improve ethical research practice, there is sometimes a disconnect between the broader moral ambitions for community engagement in the literature and guidelines on the one hand and its rather narrower practical application in health research on the other. In practice, less attention is paid to engaging communities for the ‘intrinsic’ value of showing respect and ensuring inclusive participation of community partners in research design. Rather, more attention is paid to the use of community engagement for ‘instrumental’ purposes to improve community understanding of research and ensure successful study implementation. Against this backdrop, we reviewed the literature and engaged various research stakeholders at a workshop to discuss ways of strengthening ethical engagement of communities and to develop context-relevant guidelines for community engagement in health research in Malawi.

RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.