Functional Characterisation of Surfactant Protein A as a Novel Prophylactic Means against Oncogenic HPV Infections.

Human papillomavirus (HPV) infection poses a significant health challenge, particularly in low- and middle-income countries (LMIC), where limited healthcare access and awareness hinder vaccine accessibility. To identify alternative HPV targeting interventions, we previously reported on surfactant protein A (SP-A) as a novel molecule capable of recognising HPV16 pseudovirions (HPV16-PsVs) and reducing infection in a murine cervicovaginal HPV challenge model. Building on these findings, our current study aimed to assess SP-A's suitability as a broad-spectrum HPV-targeting molecule and its impact on innate immune responses. We demonstrate SP-A's ability to agglutinate and opsonise multiple oncogenic HPV-PsVs types, enhancing their uptake and clearance by RAW264.7 murine macrophages and THP-1 human-derived immune cells. The SP-A opsonisation of HPV not only led to increased lysosomal accumulation in macrophages and HaCaT keratinocytes but also resulted in a decreased infection of HaCaT cells, which was further decreased when co-cultured with innate immune cells. An analysis of human innate immune cell cytokine profiles revealed a significant inflammatory response upon SP-A exposure, potentially contributing to the overall inhibition of HPV infection. These results highlight the multi-layered impact of SP-A on HPV, innate immune cells and keratinocytes and lay the basis for the development of alternative prophylactic interventions against diverse HPV types.

A systematic rationale for defining the significance of aircraft noise impacts.

Regulatory agencies often define strict, decibel-denominated thresholds of significance of noise impacts to protect some fraction of the residential population from exposure to highly annoying noise. Definitions of the "significance" of aircraft noise impacts and recommendations of land use "compatibility," however, typically lack detailed, systematic rationales. Instead, the definitions are justified by reference to decades-old policies that were adopted without benefit of modern understandings of noise-induced annoyance, by appeals to authority, and by generic citations of non-peer reviewed documents. Although regulatory policy decisions may properly take into consideration political and economic consequences, aspects of them are amenable to logical formalization. In particular, advances in understanding of community reaction to transportation noise now permit a systematic rationale for aircraft noise regulation. The current analyses show how regulatory policy positions can be derived from two parameters: (1) the minimal percentage of the population of a nominally average community to be protected from exposure to highly annoying noise; and (2) the percentage of all communities to which this degree of protection is intended to apply. Together with a reliable dosage-response relationship, these two parameters permit quantitatively justifiable definitions of significant noise impact.

Serum adenosine deaminase and total immunoglobulin G correlate with markers of immune activation and inversely with CD4 counts in asymptomatic, treatment-naive HIV infection.

PURPOSE: HIV-infection is characterized by aberrant immune activation and ongoing inflammation. Markers of inflammation are now recognized to have prognostic value for adverse events, independent of viral loads and CD4 counts. This study aimed to delineate a panel of affordable markers of immune activation in untreated HIV-infection that may have an impact on the management of HIV in resource-limited settings. METHODS: This was a cross-sectional study of 86 untreated newly diagnosed HIV-infected patients and 54 matched controls attending a voluntary testing clinic in Cape Town, South Africa. Serum levels of adenosine deaminase (ADA), total immunoglobulin G (IgG), soluble CD14 and lipopolysaccharide-binding protein (LBP) were measured and correlated with CD4 counts, viral loads and expression of CD38 on CD8+ T cells. RESULTS: ADA, IgG and LBP were all significantly increased in the HIV infected group (p < 0.0001) compared with uninfected controls. Soluble CD14 was also significantly increased (p = 0.0187). Furthermore, all these parameters correlated inversely with CD4 counts (r = -0.481 p < 0.0001; r = -0.561; p < 0.0001; r = -0.387 p = 0.0007 and r = -0.254 p = 0.0240, respectively). Only ADA correlated with viral load (r = 0.260 p = 0.0172). Importantly, ADA, IgG and LBP correlated directly with %CD38 on CD8+ T cells (r = 0.369 p < 0.0001; r = 0.284 p = 0.001; r = 0.408 p = 0.0006, respectively). CONCLUSION: Affordable parameters such as serum ADA and IgG correlated significantly with immune activation levels and markers of disease progression in untreated HIV-infection and therefore may add value to the management of these patients in resource-limited settings.

Development and application of a multiple linear regression model to consider the impact of weekly waste container capacity on the yield from kerbside recycling programmes in Scotland.

This article describes the development and application of a multiple linear regression model to identify how the key elements of waste and recycling infrastructure, namely container capacity and frequency of collection, affect the yield from municipal kerbside recycling programmes. The overall aim of the research was to gain an understanding of the factors affecting the yield from municipal kerbside recycling programmes in Scotland with an underlying objective to evaluate the efficacy of the model as a decision-support tool for informing the design of kerbside recycling programmes. The study isolates the principal kerbside collection service offered by all 32 councils across Scotland, eliminating those recycling programmes associated with flatted properties or multi-occupancies. The results of the regression analysis model have identified three principal factors which explain 80% of the variability in the average yield of the principal dry recyclate services: weekly residual waste capacity, number of materials collected and the weekly recycling capacity. The use of the model has been evaluated and recommendations made on ongoing methodological development and the use of the results in informing the design of kerbside recycling programmes. We hope that the research can provide insights for the further development of methods to optimise the design and operation of kerbside recycling programmes.

Assessing multiple threats to seabird populations using flesh-footed shearwaters Ardenna carneipes on Lord Howe Island, Australia as case study.

Globally, seabird populations have been in decline due to multiple threats throughout their range. Separating simultaneous pressures is challenging and can require significant amounts of data over long periods of time. We use spatial contrasts to investigate the relative importance of several drivers for the purported decline in a species listed as in decline as an example species, the Flesh-footed shearwater (Ardenna carneipes). On Lord Howe Island in the Tasman Sea, Australia, this seabird suffers from habitat loss due to housing development, intensive mortality in fisheries, plastic ingestion, and roadkill due to vehicular traffic on its breeding island. We repeated a quantitative survey of the population to ascertain whether the decline previously reported had continued and to evaluate the purported mortality sources (Reid et al. in PLoS ONE 8(4):e58230, 2013, Lavers et al. in Global Ecol Conserv 17:e00579, 2019). We measured burrow density, area of occurrence, occupancy and breeding success, integrating them with previous surveys using a Bayesian statistical model to generate longer term estimates of demographic rates. We used spatial patterns to test whether mortality on roads or proximity to human habitation was influencing population demographics. In contrast to predictions, we found the population had stabilised or increased. Characteristics such as burrow occupancy and breeding success showed little pattern, with weak evidence for impacts from road mortality and housing development. Such a data-rich approach is substantially more informative and can better support seabird conservation and management efforts does require more field-time and additional equipment than most contemporary surveys, the data is substantially more informative and can better clarify the results of efforts in seabird conservation and management.

Tear film dynamics with blinking and contact lens motion.

We develop a lubrication theory-based mathematical model that describes the dynamics of a tear film during blinking and contact lens (CL) wear. The model extends previous work on pre-corneal tear film dynamics during blinking by coupling the partial differential equation for tear film thickness to a dynamic model for CL motion. We explore different models for eyelid motion and also account for possible voluntary and involuntary globe (eyeball) rotation that may accompany blinking. Boundary conditions for mass flux at the eyelids are also adapted to account for the presence and motion of the CL. Our predictions for CL motion compare reasonably with existing data. Away from the eyelids the pre-lens tear film (PrLTF) is shifted, relative to its pre-corneal counterpart, in the direction of CL motion. Near the eyelids, the inflow/outflow of fluid under the eyelids also influences the PrLTF profile. We also compare our PrLTF dynamics to existing in vivo tear film thickness measurements.

Safety and immunogenicity of the adjunct therapeutic vaccine ID93 + GLA-SE in adults who have completed treatment for tuberculosis: a randomised, double-blind, placebo-controlled, phase 2a trial.

BACKGROUND: A therapeutic vaccine that prevents recurrent tuberculosis would be a major advance in the development of shorter treatment regimens. We aimed to assess the safety and immunogenicity of the ID93 + GLA-SE vaccine at various doses and injection schedules in patients with previously treated tuberculosis. METHODS: This randomised, double-blind, placebo-controlled, phase 2a trial was conducted at three clinical sites near Cape Town, South Africa. Patients were recruited at local clinics after receiving 4 months of tuberculosis treatment, and screened for eligibility after providing written informed consent. Participants were aged 18-60 years, BCG-vaccinated, HIV-uninfected, and diagnosed with drug-sensitive pulmonary tuberculosis. Eligible patients had completed standard treatment for pulmonary tuberculosis in the past 28 days. Participants were enrolled after completing standard treatment and randomly assigned sequentially to receive vaccine or placebo in three cohorts: 2 µg intramuscular ID93 + 2 µg GLA-SE on days 0 and 56 (cohort 1); 10 µg ID93 + 2 µg GLA-SE on days 0 and 56 (cohort 2); 2 µg ID93 + 5 µg GLA-SE on days 0 and 56 and placebo on day 28 (cohort 3); 2 µg ID93 + 5 µg GLA-SE on days 0, 28, and 56 (cohort 3); or placebo on days 0 and 56 (cohorts 1 and 2), with the placebo group for cohort 3 receiving an additional injection on day 28. Randomisation was in a ratio of 3:1 for ID93 + GLA-SE and saline placebo in cohorts 1 and 2, and in a ratio of 3:3:1 for (2 ×) ID93 + GLA-SE, (3 ×) ID93 + GLA-SE, and placebo in cohort 3. The primary outcomes were safety and immunogenicity (vaccine-specific antibody response and T-cell response). For the safety outcome, participants were observed for 30 min after each injection, injection site reactions and systemic adverse events were monitored until day 84, and serious adverse events and adverse events of special interest were monitored for 6 months after the last injection. Vaccine-specific antibody responses were measured by serum ELISA, and T-cell responses after stimulation with vaccine antigens were measured in cryopreserved peripheral blood mononuclear cells specimens using intracellular cytokine staining followed by flow cytometry. This study is registered with ClinicalTrials.gov, number NCT02465216. FINDINGS: Between June 17, 2015, and May 30, 2016, we assessed 177 patients for inclusion. 61 eligible patients were randomly assigned to receive: saline placebo (n=5) or (2 ×) 2 µg ID93 + 2 µg GLA-SE (n=15) on days 0 and 56 (cohort 1); saline placebo (n=2) or (2 ×) 10 µg ID93 + 2 µg GLA-SE (n=5) on days 0 and 56 (cohort 2); saline placebo (n=5) on days 0, 28 and 56, or 2 µg ID93 + 5 µg GLA-SE (n=15) on days 0 and 56 and placebo injection on day 28, or (3 ×) 2 µg ID93 + 5 µg GLA-SE (n=14) on days 0, 28, and 56 (cohort 3). ID93 + GLA-SE induced robust and durable antibody responses and specific, polyfunctional CD4 T-cell responses to vaccine antigens. Two injections of the 2 µg ID93 + 5 µg GLA-SE dose induced antigen-specific IgG and CD4 T-cell responses that were significantly higher than those with placebo and persisted for the 6-month study duration. Mild to moderate injection site pain was reported after vaccination across all dose combinations, and induration and erythema in patients given 2 µg ID93 + 5 µg GLA-SE in two or three doses. One participant had grade 3 erythema and induration at the injection site. No vaccine-related serious adverse events were observed. INTERPRETATION: Vaccination with ID93 + GLA-SE was safe and immunogenic for all tested regimens. These data support further evaluation of ID93 + GLA-SE in therapeutic vaccination strategies to improve tuberculosis treatment outcomes. FUNDING: Wellcome Trust (102028/Z/13/Z).

Immune Phenotype and Functionality of Mtb-Specific T-Cells in HIV/TB Co-Infected Patients on Antiretroviral Treatment.

The performance of host blood-based biomarkers for tuberculosis (TB) in HIV-infected patients on antiretroviral therapy (ART) has not been fully assessed. We evaluated the immune phenotype and functionality of antigen-specific T-cell responses in HIV positive (+) participants with TB (n = 12) compared to HIV negative (-) participants with either TB (n = 9) or latent TB infection (LTBI) (n = 9). We show that the cytokine profile of Mtb-specific CD4+ T-cells in participants with TB, regardless of HIV status, was predominantly single IFN-γ or dual IFN-γ/ TNFα. Whilst ESAT-6/CFP-10 responding T-cells were predominantly of an effector memory (CD27-CD45RA-CCR7-) profile, HIV-specific T-cells were mainly of a central (CD27+CD45RA-CCR7+) and transitional memory (CD27+CD45RA+/-CCR7-) phenotype on both CD4+ and CD8+ T-cells. Using receiving operating characteristic (ROC) curve analysis, co-expression of CD38 and HLA-DR on ESAT-6/CFP-10 responding total cytokine-producing CD4+ T-cells had a high sensitivity for discriminating HIV+TB (100%, 95% CI 70-100) and HIV-TB (100%, 95% CI 70-100) from latent TB with high specificity (100%, 95% CI 68-100 for HIV-TB) at a cut-off value of 5% and 13%, respectively. TB treatment reduced the proportion of Mtb-specific total cytokine+CD38+HLA-DR+ CD4+ T-cells only in HIV-TB (p = 0.001). Our results suggest that co-expression of CD38 and HLA-DR on Mtb-specific CD4+ T-cells could serve as a TB diagnosis tool regardless of HIV status.

Combining radar and direct observation to estimate pelican collision risk at a proposed wind farm on the Cape west coast, South Africa.

Pre-construction assessments of bird collision risk at proposed wind farms are often confounded by insufficient or poor quality data describing avian flight paths through the development area. These limitations can compromise the practical value of wind farm impact studies. We used radar- and observer-based methods to quantify great white pelican flights in the vicinity of a planned wind farm on the Cape west coast, South Africa, and modelled turbine collision risk under various scenarios. Model outputs were combined with pre-existing demographic data to evaluate the possible influence of the wind farm on the pelican population, and to examine impact mitigation options. We recorded high volumes of great white pelican movement through the wind farm area, coincident with the breeding cycle of the nearby colony and associated with flights to feeding areas located about 50 km away. Pelicans were exposed to collision risk at a mean rate of 2.02 High Risk flights.h-1. Risk was confined to daylight hours, highest during the middle of the day and in conditions of strong north-westerly winds, and 82% of High Risk flights were focused on only five of the proposed 35 turbine placements. Predicted mean mortality rates (22 fatalities.yr-1, 95% Cl, 16-29, with average bird and blade speeds and 95% avoidance rates) were not sustainable, resulting in a negative population growth rate (λ = 0.991). Models suggested that removal of the five highest risk turbines from the project, or institution of a curtailment regimen that shuts down at least these turbines at peak traffic times, could theoretically reduce impacts to manageable levels. However, in spite of the large quantities of high quality data used in our analyses, our collision risk model remains compromised by untested assumptions about pelican avoidance rates and uncertainties about the existing dynamics of the pelican population, and our findings are probably not reliable enough to ensure sustainable development.

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.

Re-examining mortality sources and population trends in a declining seabird: using Bayesian methods to incorporate existing information and new data.

The population of flesh-footed shearwaters (Puffinus carneipes) breeding on Lord Howe Island was shown to be declining from the 1970's to the early 2000's. This was attributed to destruction of breeding habitat and fisheries mortality in the Australian Eastern Tuna and Billfish Fishery. Recent evidence suggests these impacts have ceased; presumably leading to population recovery. We used Bayesian statistical methods to combine data from the literature with more recent, but incomplete, field data to estimate population parameters and trends. This approach easily accounts for sources of variation and uncertainty while formally incorporating data and variation from different sources into the estimate. There is a 70% probability that the flesh-footed shearwater population on Lord Howe continued to decline during 2003-2009, and a number of possible reasons for this are suggested. During the breeding season, road-based mortality of adults on Lord Howe Island is likely to result in reduced adult survival and there is evidence that breeding success is negatively impacted by marine debris. Interactions with fisheries on flesh-footed shearwater winter grounds should be further investigated.