The Evolutionary Pathway to Virulence of an RNA Virus.

Paralytic polio once afflicted almost half a million children each year. The attenuated oral polio vaccine (OPV) has enabled world-wide vaccination efforts, which resulted in nearly complete control of the disease. However, poliovirus eradication is hampered globally by epidemics of vaccine-derived polio. Here, we describe a combined theoretical and experimental strategy that describes the molecular events leading from OPV to virulent strains. We discover that similar evolutionary events occur in most epidemics. The mutations and the evolutionary trajectories driving these epidemics are replicated using a simple cell-based experimental setup where the rate of evolution is intentionally accelerated. Furthermore, mutations accumulating during epidemics increase the replication fitness of the virus in cell culture and increase virulence in an animal model. Our study uncovers the evolutionary strategies by which vaccine strains become pathogenic and provides a powerful framework for rational design of safer vaccine strains and for forecasting virulence of viruses. VIDEO ABSTRACT.

Food Systems Interventions for Nutrition: Lessons from 6 Program Evaluations in Africa and South Asia.

Although there is growing global momentum behind food systems strategies to improve planetary and human health-including nutrition-there is limited evidence of what types of food systems interventions work. Evaluating these types of interventions is challenging due to their complex and dynamic nature and lack of fit with standard evaluation methods. In this article, we draw on a portfolio of 6 evaluations of food systems interventions in Africa and South Asia that were intended to improve nutrition. We identify key methodological challenges and formulate recommendations to improve the quality of such studies. We highlight 5 challenges: a lack of evidence base to justify the intervention, the dynamic and multifaceted nature of the interventions, addressing attribution, collecting or accessing accurate and timely data, and defining and measuring appropriate outcomes. In addition to more specific guidance, we identify 6 cross-cutting recommendations, including a need to use multiple and diverse methods and flexible designs. We also note that these evaluation challenges present opportunities to develop new methods and highlight several specific needs in this space.

Climate change related phenological decoupling in species belonging to the Betulaceae family.

Betulaceae species are anemophilous, and allergens from their pollen are a major cause of respiratory allergies in temperate areas where they are widely distributed. It is expected that, due to the strong influence of temperature on Betulaceae phenology, global warming will impact both the distribution and phenology of these species during the coming decades. This study examines potential decoupling of flowering and leafing phenophases in Betulaceae species (i.e. Alnus glutinosa, Betula pendula and Corylus avellana) over long-term (1951-2015) and as shorter (15-year) periods. Phenological phases for flowering and leaf unfolding of Betulaceae species from the Pan-European Phenology (PEP725) database were examined along with maximum and minimum daily temperature data for the periods September-October-November (SON), December-January-February (DJF) and March-April-May (MAM). Significant increases in temperature since 1951 have been recorded in the relevant chilling and forcing periods. Both flowering and leaf unfolding phenophases are advancing, but flowering is advancing faster than leaf unfolding. This is increasing the time between phenophases, although analysis of 15-year periods shows that the pattern of change was not constant. The results presented here represent the most comprehensive analysis of flowering and leaf unfolding phenophases of Betulaceae species using the PEP725 database to date. It is expected that these changes to Betulaceae phenology will continue and that global warming-related phenological decoupling will increase plant stress in Betulaceae populations in central Europe.

Investigating Palestinian in-service teachers' beliefs about the integration of information and communication technology (ICT) into teaching English.

The purpose of this study was to look into how Information and Communication Technology (ICT) is used in teaching English language from the point-of-view of English language teachers in Palestine. A quantitative approach was employed to collect data from 780 language school teachers from 260 schools who participated in a course project utilizing ICT in English as a Foreign Language teaching (TEFL). These participants responded to a questionnaire survey about the effects of the Covid-19 epidemic on language education and how they dealt with these. We statistically analysed the responses through four domains: the use of ICT in students' lives; the use of ICT in education generally; the use of ICT to support learning and teaching in EFL; and teachers' perceived skills for using ICT in education. Results indicated that English language teachers in Palestinian public schools believed that ICT has clear potential to support the learning of English, but that there remain barriers to its implementation. Teachers feel equipped to use ICT but would like to see a greater emphasis on training in order to maximise their teaching.

Clinical Spectrum of Severe Acute Respiratory Syndrome Coronavirus 2 Infection and Protection From Symptomatic Reinfection.

BACKGROUND: There are few data on the full spectrum of disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection across the lifespan from community-based or nonclinical settings. METHODS: We followed 2338 people in Managua, Nicaragua, aged <94 years from March 2020 through March 2021. SARS-CoV-2 infection was identified through real-time reverse transcription polymerase chain reaction (RT-PCR) or through enzyme-linked immunosorbent assay. Disease presentation was assessed at the time of infection or retrospectively by survey at the time of blood collection. RESULTS: There was a large epidemic that peaked between March and August 2020. In total, 129 RT-PCR-positive infections were detected, for an overall incidence rate of 5.3 infections per 100 person-years (95% confidence interval [CI], 4.4-6.3). Seroprevalence was 56.7% (95% CI, 53.5%-60.1%) and was consistent from age 11 through adulthood but was lower in children aged ≤10 years. Overall, 31.0% of the infections were symptomatic, with 54.7% mild, 41.6% moderate, and 3.7% severe. There were 2 deaths that were likely due to SARS-CoV-2 infection, yielding an infection fatality rate of 0.2%. Antibody titers exhibited a J-shaped curve with respect to age, with the lowest titers observed among older children and young adults and the highest among older adults. When compared to SARS-CoV-2-seronegative individuals, SARS-CoV-2 seropositivity at the midyear sample was associated with 93.6% protection from symptomatic reinfection (95% CI, 51.1%-99.2%). CONCLUSIONS: This population exhibited a very high SARS-CoV-2 seropositivity with lower-than-expected severity, and immunity from natural infection was protective against symptomatic reinfection.

Patterned achromatic elliptical polarizer for short-wave infrared imaging polarimetry.

Short-wave infrared (SWIR) imaging polarimetry has widespread applications in telecommunication, medical imaging, surveillance, remote-sensing, and industrial metrology. In this work, we design, fabricate, and test an achromatic SWIR elliptical polarizer, which is a key component of SWIR imaging polarimetry. The elliptical polarizer is made of a patterned linear polarizer and a patterned optical elliptical retarder. The linear polarizer is a wire grid polarizer. The elliptical retarder is constructed with three layers of nematic phase A-plate liquid crystal polymer (LCP) films with different fast axis orientations and physical film thicknesses. For each LCP layer, four arrays of hexagonal patterns with individual fast-axis orientations are realized utilizing selective linearly polarized ultraviolet (UV) irradiation on a photo-alignment polymer film. The Mueller matrices of the optical filters were measured in the wavelength range 1000 nm to 1600 nm and compared with theory. Our results demonstrate the functionality and quality of the patterned retarders with normalized analyzer vector parameter deviation below 7% over this wavelength range. To the best of our knowledge, this work represents the first polymer-based patterned elliptical polarizer for SWIR polarimetry imaging applications.

Real-time automatic detection of starch particles in ambient air.

Considerable amounts of starch granules can be present in the atmosphere from both natural and anthropogenic sources. The aim of this study is to investigate the variability and potential origin of starch granules in ambient air recorded at six cities situated in a region with dominantly agricultural land use. This is achieved by using a combination of laser spectroscopy bioaerosol measurements with 1 min temporal resolution, traditional volumetric Hirst type bioaerosol sampling and atmospheric modelling. The analysis of wind roses identified potential sources of airborne starch (i.e., cereal grain storage facilities) in the vicinity of all aerobiological stations analysed in this study. The analysis of the CALPUFF dispersion model confirmed that emission of dust from the location of storage towers situated about 2.5 km north of the aerobiological station in Novi Sad is a plausible source of high airborne concentrations of starch granules. This study is important for environmental health since it contributes body of knowledge about sources, emission, and dispersion of airborne starch, known to be involved in phenomena such as thunderstorm-triggered asthma. The presented approach integrates monitoring and modelling, and provides a roadmap for examining a variety of bioaerosols previously considered to be outside the scope of traditional aerobiological measurements.

Prevention and control of mosquito-borne arboviral diseases: lessons learned from a school-based intervention in Brazil (Zikamob).

BACKGROUND: Since the 1980s, when dengue was reintroduced in Brazil, outbreaks and epidemics caused by different arbovirus strains transmitted by vector mosquitoes such as Aedes aegypti have been an annual occurrence. The aim of this study was to evaluate the behavioural change of high school students and teachers who participated in an educational intervention for the prevention and vector control of arboviral diseases. METHODS: In this school-based intervention, a self-reported questionnaire was used in a pre-post intervention methodology to assess environmental risk factors, sociodemographic variables and to measure attitudes and behaviours. In all, 883 high school students and teachers from the city of Campina Grande, in the state of Paraíba, northeastern Brazil, participated. The e-health intervention consisted of a competition between schools to comply with preventive actions via content production for social networks, and the monitoring was performed over a period of three months through the ZikaMob software developed by the researchers. RESULTS: Out of the 883 survey participants, 690 were students ranging in age from 14 to 41 years, with an average of 17 ± 2 years; and 193 were teachers from 22 to 64 years old, averaging 38 ± 9 years. The analysis of the data shows that significant differences in most of the target behaviours were apparent after the intervention, with an increase of about 10% in the performance of inspection actions; a 7% greater separation of recyclables and a 40% increase in the screening of windows among students. Students showed lower fear of, and a lower self-perception of the risk of, acquiring arboviruses than teachers on average. CONCLUSIONS: ZikaMob is an innovative strategy with the potential to be replicated in any location that has an internet network and can involve an unlimited number of participants.

A comprehensive aerobiological study of the airborne pollen in the Irish environment.

Respiratory allergies triggered by pollen allergens represent a significant health concern to the Irish public. Up to now, Ireland has largely refrained from participating in long-term aerobiological studies. Recently, pollen monitoring has commenced in several sampling locations around Ireland. The first results of the pollen monitoring campaigns for Dublin (urban) and Carlow (rural) concerning the period 2017-2019 and 2018-2019, respectively, are presented herein. Additional unpublished pollen data from 1978-1980 and, 2010-2011 were also incorporated in creating the first pollen calendar for Dublin. During the monitoring period over 60 pollen types were identified with an average Annual Pollen Integral (APIn) of 32,217 Pollen × day/m3 for Dublin and 78,411 Pollen × day/m3 for Carlow. The most prevalent pollen types in Dublin were: Poaceae (32%), Urticaceae (29%), Cupressaceae/Taxaceae (11%), Betula (10%), Quercus (4%), Pinus (3%), Fraxinus (2%), Alnus (2%) and Platanus (1%). The predominant pollen types in Carlow were identified as Poaceae (70%), Urticaceae (12%), Betula (10%), Quercus (2%), Fraxinus (1%) and Pinus (1%). These prevalent pollen types increased in annual pollen concentration in both locations from 2018 to 2019 except for Fraxinus. Although higher pollen concentrations were observed for the Carlow (rural) site a greater variety of pollen types were identified for the Dublin (urban) site. The general annual trend in the pollen season began with the release of tree pollen in early spring, followed by the release of grass and herbaceous pollen which dominated the summer months with the annual pollen season coming to an end in October. This behaviour was illustrated for 21 different pollen types in the Dublin pollen calendar. The correlation between ambient pollen concentration and meteorological parameters was also examined and differed greatly depending on the location and study year. A striking feature was a substantial fraction of the recorded pollen sampled in Dublin did not correlate with the prevailing wind directions. However, using non-parametric wind regression, specific source regions could be determined such as Alnus originating from the Southeast, Betula originating from the East and Poaceae originating from the Southwest. Supplementary Information: The online version contains supplementary material available at 10.1007/s10453-022-09751-w.

Evaluation of an inner city HIV pre-exposure prophylaxis service tailored to the needs of people who inject drugs.

OBJECTIVES: HIV prevention strategies including pre-exposure prophylaxis (PrEP) must reach all in need to achieve elimination of transmission by 2030. Mainstream provision may inadvertently exclude key populations. Incidence of HIV in people who inject drugs (PWID) in Glasgow, Scotland's largest city, is increasing, partly due to sexual transmission. Scotland provides publicly funded oral PrEP for individuals at sexual risk of HIV through sexual health services; however, uptake by PWID has been negligible. We developed a tailored outreach PrEP service based in the local homeless health centre. We used active case finding, flexibility of assessment location, supervised community daily dispensing and active follow-up to optimise uptake and adherence. We describe a two-year service evaluation. METHODS: We reviewed the case records of all PWID identified by the outreach team as being at higher risk of sexual acquisition for whom PrEP was considered between November 2018 and November 2020. Evaluation focused on PrEP uptake, adherence and monitoring. We conducted a descriptive statistical analysis. RESULTS: Of 41 PWID assessed as eligible, 32 (78.0%) commenced PrEP. The proportion of PrEP-covered days was 3320/3400 days (97.6%); 31/32 (96.9%) had regular HIV serology monitoring. The service was feasible to run, but it relied on outreach provision and liaison with other services. DISCUSSION: Tailored PrEP services can reach PWID effectively. Uptake and adherence were high but the model was resource-intensive. Appropriately tailored PrEP delivery may be required to meet the needs of this and other key populations who experience barriers to accessing mainstream services.

Effects of future climate change on birch abundance and their pollen load.

Climate change impacts on the structure and function of ecosystems will worsen public health issues like allergic diseases. Birch trees (Betula spp.) are important sources of aeroallergens in Central and Northern Europe. Birches are vulnerable to climate change as these trees are sensitive to increased temperatures and summer droughts. This study aims to examine the effect of climate change on airborne birch pollen concentrations in Central Europe using Bavaria in Southern Germany as a case study. Pollen data from 28 monitoring stations in Bavaria were used in this study, with time series of up 30 years long. An integrative approach was used to model airborne birch pollen concentrations taking into account drivers influencing birch tree abundance and birch pollen production and projections made according to different climate change and socioeconomic scenarios. Birch tree abundance is projected to decrease in parts of Bavaria at different rates, depending on the climate scenario, particularly in current centres of the species distribution. Climate change is expected to result in initial increases in pollen load but, due to the reduction in birch trees, the amount of airborne birch pollen will decrease at lower altitudes. Conversely, higher altitude areas will experience expansions in birch tree distribution and subsequent increases in airborne birch pollen in the future. Even considering restrictions for migration rates, increases in pollen load are likely in Southwestern areas, where positive trends have already been detected during the last three decades. Integrating models for the distribution and abundance of pollen sources and the drivers that control birch pollen production allowed us to model airborne birch pollen concentrations in the future. The magnitude of changes depends on location and climate change scenario.

Mathematical method for designing superresolution lenses using superoscillations.

We use a new mathematical method to design a superresolution lens using a superoscillation technique based on polynomial roots. We walk through an example of the method using simulations. Our method allows for ease of design by being mathematically and conceptually simpler than other methods.

Review of British Standard BS 4094-1:1966 Part 1: data on shielding from gamma radiation.

British Standard BS 4094-1:1966 Part 1 (entitled 'Data on Shielding from Ionizing Radiation Part 1: Shielding from Gamma Radiation') provides a series of transmission curves (the Figure 2 series) which illustrate the attenuation of gamma radiation from eleven isotopes through a variety of absorber media. As such it is widely utilised across the nuclear industry and other sectors. However, British Standard BS4094 1:1966 was collated over 50 years ago when both computer codes and nuclear data were significantly less advanced than they are today. This paper reproduces the British Standard Figure 2 series in order to benchmark it against modern computer codes (specifically MCNP 6.2 and RANKERN) and data taken from more modern nuclear data libraries. The results show good agreement in the majority of cases. However, there are some significant discrepancies in a number of isotope / absorber combinations and in some of these cases British Standard BS 4094-1:1966 Part 1 may not be conservative. This paper concludes that a modern revision to British Standard BS 4094 1:1966 Part 1 would be appropriate and timely.

Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava) 1.

Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.

Histopathological Findings in Cynomolgus Macaques ( Macaca fascicularis) Consistent with Secondary Immunological Reaction to Biotherapeutics with an Emphasis on the CNS and Eye.

Biotherapeutics are pharmaceutical products derived from or synthesized by biological systems. Such molecules carry the potential for immunogenicity which may lead to adverse immune responses. The cynomolgus macaque ( Macaca fascicularis) is the species of choice in nonclinical safety assessment of biotherapeutics. The main aim of this study was to confirm whether mononuclear cell infiltrates at specific locations represent a generic effect of biotherapeutics, and therefore the result of their immunogenicity. Following a review of microscopic findings in studies conducted over a 10-year period at one test facility, 15% of biotherapeutics were reported to have such findings. The most commonly affected site was the choroid plexus and less frequently the meninges and ciliary body. The reporting of such findings as test article-related becomes more subjective as the severity and incidence decreases. To assess the accuracy of such associations, a mathematical approach was employed to determine the probability of obtaining the observed results by chance. There was good agreement between this approach and the original findings. In addition to an increased number and size of mononuclear cell infiltrates in the brain, biotherapeutic administration was strongly associated with the presence of plasma cells and eosinophils.

Best available science still supports an ancient common origin of Devils Hole and Devils Hole pupfish.

The age of DHP and how pupfish colonized Devils Hole have always been a topic of interest. Recently, two different publications (Martin, Crawford, Turner, & Simons, & Saglam et al., ) tackled this issue using genomic data sets and demographic models but came to widely different conclusions. In their comment, Martin and Höhne () argue that our results (Saglam et al., ) were misleading because we used inappropriate calibration information and biased a priori assumptions. They then re-analysed our data using a "biologically informed" mutation rate prior and concluded that our data support a much younger age of DHP (12.6 kya) as opposed to 60 kya reported in our study. Below we will summarize why their arguments do not hold up and explore some of the inconsistencies between their claims and what was actually presented in our study. Furthermore, we will demonstrate their re-analyses provide no new information compared to what was presented in our original manuscript and reinforce our estimate of a 60 kya divergence of DHP as outweighing competing hypotheses.

Cross-sensitization to Artemisia and Ambrosia pollen allergens in an area located outside of the current distribution range of Ambrosia.

INTRODUCTION: The role of long-distance transported (LDT) Ambrosia pollen in inducing new sensitization and affecting sensitization rates in Artemisia-sensitized patients is unclear. AIM: The aim of this study was to estimate the degree of cross-sensitization to Ambrosia/Artemisia allergens in citizens of Poznan (Western Poland). This area is covered by extensive Artemisia populations but does not currently have local Ambrosia populations. MATERIAL AND METHODS: Sera of 119 patients were tested by fluoroenzyme immunoassay (CAP-FEIA system) against pollen allergen extracts of Artemisia vulgaris and Ambrosia artemisiifolia, an allergenic component of A. vulgaris (nArt v 1), and an allergenic component of A. artemisiifolia (nAmb a 1). Skin prick tests (SPTs, n = 86) were performed with pollen allergen extracts of A. vulgaris and A. artemisiifolia. Artemisia and Ambrosia pollen in ambient air was collected (1996-2013) by a Hirst type volumetric trap sited at roof level (33 m). RESULTS: The SPT showed that the prevalence of sensitization to Ambrosia and Artemisia pollen exceeded 3.5%, and 10.5%, respectively. The measurements of IgE in blood serum (CAP-FEIA) revealed that among Ambrosia-sensitized patients 90.1% (20/22 patients) were concomitantly sensitized to Artemisia. 59.1% (13/22) of these patients reacted to nArt v 1, suggesting primary sensitization to Artemisia pollen. Only 2 (9.1%) patients were mono-sensitized to Ambrosia pollen extract, but surprisingly not to nAmb a 1. CONCLUSIONS: The LDT Ambrosia pollen had a negligible effect on the rate of sensitization to Ambrosia allergens in Poznan and did not increase the prevalence of sensitization to Artemisia pollen in this region. However, the majority of patients showing hypersensitization to Artemisia pollen might also present symptoms during elevated episodes of LDT of Ambrosia pollen.

Aerobiology in the International Journal of Biometeorology, 1957-2017.

Aerobiology and biometeorology are related fields. Here we provide a broad review of aerobiology articles published in the International Journal of Biometeorology (IJB) over the past 60 years. We consider how the quantity of such work has varied over this period as well as which regions and countries have been the focus of such work, and where there is a relative paucity. We then focus on a number of highlights and themes in this research, including aerobiology and climate change and aerobiological modelling and forecasting. While much of the article focusses on airborne pollen research, we also discuss the extent to which other airborne organic particles such as fungal spores and bacteria have been the focus of research published in IJB. Also considered are knowledge gaps and research needs and priorities with respect to the field of aerobiology. While the IJB has been one of the main platforms for presenting aerobiological research over recent decades, the article highlights the need for the field of aerobiology to embrace new sampling technologies such as spectral analysis and next-generation sequencing to identify and quantify airborne biological particles.

Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish.

The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m(2) pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high-resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20-10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration.

Construction of arbitrary vortex and superoscillatory fields.

Superoscillations, oscillations of a bandlimited signal at frequencies greater than its band limit, have been verified both theoretically and experimentally. The design of such superoscillatory waves, however, has typically relied on complicated mathematics. We introduce a simple Fourier method to construct superoscillations in the transverse plane of an optical field in the form of optical vortices.