bluuebunny/crossref_metadata_2025 huggingface dataset:
Biodiversity and the Recreational Value of Green Infrastructure in England
Authors: Murkin Katherine , Shiode Narushige , Shiode Shino , Kidd David
Published: February 2023

Green infrastructure refers to connected corridors of greenspaces within and beyond urban areas. It provides sustainable ecosystem goods and services for people and wildlife, enhancing their wellbeing and protecting them against climatic extremes. However, the exact contributing factors to the betterment of green infrastructure are not systematically examined at a national level. This study aims to identify what helps improve biodiversity and the recreational value of green infrastructure. The study uses hotspot analysis, ordinary least squares (OLS) regression and geographically weighted regression (GWR) to understand the spatial patterns of the relevant variables and outcomes. Findings suggest that high wildlife species richness was reported in Forestry Commission woodlands and country parks, whilst doorstep greens and village greens returned poor species richness. The recreational value of greenspace was affected the most by certain types of greenspace (e.g., woodlands) as well as the percentage of urban cover. They indicate that biodiversity is generally high in areas away from urban centres, while access to greenspace in an urban space brings us high recreational value. These results indicate that green infrastructure is a complex system that requires the right balance between different priorities and services.
On the Polarization Dependence of Two-Photon Processes including X-ray Scattering
Authors: Manakov Nikolai L. , Meremianin Alexei V.
Published: February 2023

The polarization dependence of the cross sections of two-photon transitions including X-ray scattering was analyzed. We developed the regular approach to the derivation of the polarization parameters of photoprocesses. Our approach is based on the tensor representation of the photon density matrix, which is written in terms of the unit vectors directed along the major axis of the polarization ellipse (ϵˆ) and the photon propagation (kˆ). Explicit expressions for the product of two photon density matrices were derived. As an example, the parametrization of the polarization dependence of the X-ray scattering by closed-shell atoms is given both in terms of (i) scalar products of photon vectors ϵˆ1,2, kˆ1,2 and (ii) X-ray Stokes parameters. We discuss the applicability of the atomic scattering for the measurement of the polarization of X-rays.
Computational Simulation and Parametric Analysis of the Effectiveness of Ternary Nano-composites in Improving Magneto-Micropolar Liquid Heat Transport Performance
Authors: Alwawi Firas A. , Swalmeh Mohammed Z. , Hamarsheh Abdulkareem Saleh
Published: February 2023

This numerical analysis aims to observe and analyze the combined convection characteristics of the micropolar tri-hybrid nano-liquid that moves around a cylindrical object, and, in addition, to compare its thermal behavior to that of hybrid and mono nano-fluids. For this purpose, the problem is modeled by developing the Tiwari and Das models, then the governing model is converted into dimensionless expressions, and finally, the problem is solved using the Keller box approximation. The current findings are compared with previously published results to show that the present method is sufficiently accurate for physical and engineering applications. By examining and analyzing the extent to which skin friction, the Nusselt number, velocity, angular velocity, and temperature are affected by some critical factors, the following points are revealed: A greater value of the micropolar and magnetic factors can result in curtailing the heat transmission rate, velocity, and angular velocity. Higher values of the mixed convection factor can contribute to a better rate of energy transfer and can grant the micropolar tri-hybrid nano-liquid a higher velocity. Regardless of the influencing factors, the maximum value of all considered physical groups is achieved by using ternary hybrid nano-liquids.
A Comparative Analysis of Fractional-Order Fokker–Planck Equation
Authors: Mofarreh Fatemah , Khan Asfandyar , Shah Rasool , Abdeljabbar Alrazi
Published: February 2023

The importance of partial differential equations in physics, mathematics and engineering cannot be emphasized enough. Partial differential equations are used to represent physical processes, which are then solved analytically or numerically to examine the dynamical behaviour of the system. The new iterative approach and the Homotopy perturbation method are used in this article to solve the fractional order Fokker–Planck equation numerically. The Caputo sense is used to characterize the fractional derivatives. The suggested approach’s accuracy and applicability are demonstrated using illustrations. The proposed method’s accuracy is expressed in terms of absolute error. The proposed methods are found to be in good agreement with the exact solution of the problems using graphs and tables. The results acquired using the given approaches are also obtained at various fractional orders of the derivative. It is observed from the graphs and tables that fractional order solutions converge to an integer solution when the fractional orders approach the integer-order of the problems. The tabular and graphical view for the given problems is obtained through Maple. The presented approaches can be applied to existing non-linear fractional partial differential equations due to their accurate, simple and straightforward implementation.
Revisiting the Schrödinger–Dirac Equation
Authors: Fleury Nicolas , Hammad Fayçal , Sadeghi Parvaneh
Published: February 2023

In flat spacetime, the Dirac equation is the “square root” of the Klein–Gordon equation in the sense that, by applying the square of the Dirac operator to the Dirac spinor, one recovers the equation duplicated for each component of the spinor. In the presence of gravity, applying the square of the curved-spacetime Dirac operator to the Dirac spinor does not yield the curved-spacetime Klein–Gordon equation, but instead yields the Schrödinger–Dirac covariant equation. First, we show that the latter equation gives rise to a generalization to spinors of the covariant Gross–Pitaevskii equation. Then, we show that, while the Schrödinger–Dirac equation is not conformally invariant, there exists a generalization of the equation that is conformally invariant but which requires a different conformal transformation of the spinor than that required by the Dirac equation. The new conformal factor acquired by the spinor is found to be a matrix-valued factor obeying a differential equation that involves the Fock–Ivanenko line element. The Schrödinger–Dirac equation coupled to the Maxwell field is then revisited and generalized to particles with higher electric and magnetic moments while respecting gauge symmetry. Finally, Lichnerowicz’s vanishing theorem in the conformal frame is also discussed.
Fermatean Fuzzy CODAS Approach with Topology and Its Application to Sustainable Supplier Selection
Authors: Farid Hafiz Muhammad Athar , Bouye Mohamed , Riaz Muhammad , Jamil Nimra
Published: February 2023

A Fermatean fuzzy set (FFS) is a reliable method for representing uncertainty in “multi-criteria decision-making” (MCDM). This research seeks to examine the topological properties of FFSs and to establish the notion of “Fermatean fuzzy topology” (FFT). An FFT is the generalisation of existing fuzzy topologies. Several aspects of FFT are examined and various novel concepts are proposed, which include Fermatean fuzzy α-continuity between FFTSs and Fermatean fuzzy connectedness. To deal multiple challenges in sustainable supply chain management, a Fermatean fuzzy “combinative distance-based assessment” (CODAS) method was developed. The proposed FF CODAS technique involves various key features for MCDM. Firstly, a known reputation vector or equal expert weights is determined based on the reputation, experience and qualifications of the experts. Secondly, the Fermatean fuzzy direct rating approach is used to establish the relative relevance of criteria based on the expert group’s evaluation preferences. Thirdly, the Fermatean fuzzy CODAS approach is used to construct alternative orderings based on their assessment scores. Finally, an application is developed to show the benefit of the suggested supplier selection approach. Additionally, the symmetry of an optimal decision in application is carried out by a comparison analysis of the suggested models with some existing models.
Coincidence Theorems under Generalized Nonlinear Relational Contractions
Authors: Altaweel Nifeen Hussain , Eljaneid Nidal H. E. , Mohammed Hamid I. A. , Alanazi Ibtisam M. , Khan Faizan Ahmad
Published: February 2023

After the appearance of relation-theoretic contraction principle due to Alam and Imdad, the domain of fixed point theory applied to relational metric spaces has attracted much attention. Existence and uniqueness of fixed/coincidence points satisfying the different types of contractivity conditions in the framework of relational metric space have been studied in recent times. Such results have the great advantage to solve certain types of matrix equations and boundary value problems for ordinary differential equations, integral equations and fractional differential equations. This article is devoted to proving the coincidence and common fixed point theorems for a pair of mappings (T,S) employing relation-theoretic (ϕ,ψ)-contractions in a metric space equipped with a locally finitely T-transitive relation. Our results improve, modify, enrich and unify several existing coincidence points as well as fixed point results. Several examples are provided to substantiate the utility of our results.
How Are a Firm’s Strategic Motives for Environmental Innovation Impeded? The Negative Influences of Institutional Pressures
Authors: Ra Keehyuk , Hong Suengjae , Yang Daegyu
Published: February 2023

In recent years, firms are intensively being asked to build up the capabilities of dealing with environmental issues. While most firms are proactively inspired by their strategic motives for the environmental innovations, they are also exposed to the external pressures for environmental innovations that are institutionally established. This study is an early attempt to theoretically examine how firms’ strategic motives for environmental innovation are affected by the institutional pressures of environmental issues in a single empirical setting. Based on the institutional theory, this study suggests two types of institutional pressures — regulative and normative pressures— and proposes the conflicting effects of the strategic motive and the institutional pressures in the firms’ activities concerning environmental innovation. In addition to the test of the interrelated effects of strategic motives and institutional pressures, this study also investigates how small and medium-sized enterprises (SMEs) differ in their efforts to realize the strategic motives for environmental innovation, in contrast to large companies. The Korean Innovation Survey was used to test the proposed hypotheses. The findings of the analysis support all the hypotheses about the negative influences of institutional pressures on the effect of strategic motives on environmental innovation actions. Finally, the theoretical contributions and managerial implications are discussed.
Simplifying the Complexity in the Problem of Choosing the Best Private-Sector Partner
Authors: Qiu Peiyao , Sorourkhah Ali , Kausar Nasreen , Cagin Tonguc , Edalatpanah Seyyed Ahmad
Published: February 2023

Governments frequently partner with the private sector to provide infrastructure and public services. These cooperations, known as public–private partnerships (PPPs), have often failed. Sometimes, due to the problem’s complexity, the public sector cannot choose the right partner for these projects, which is one of the main reasons for failures. Complexity in such problems is associated with a large number of indicators, imprecise judgments of decision-makers or problem owners, and the unpredictability of the environment (under conditions of uncertainty). Therefore, presenting a simplified algorithm for this complicated process is the primary goal of the current research so that it can consider the problem’s various dimensions. While many researchers address the critical risk factors (CRFs) and others focus on key performance indicators (KPIs), this research has considered both CRFs and KPIs to choose the best private-sector partner. In addition, we used single-valued neutrosophic sets (SVNSs) to collect decision-makers’ views, which can handle ambiguous, incomplete, or imprecise information. Next, by defining the ideal alternative and using the similarity measure, we specified the ranks of the alternative. Additionally, to face the uncertain environment, we examined the performance of options in four future scenarios. The steps of the proposed algorithm are explained in the form of a numerical example. The results of this research showed that by employing a simple algorithm, even people who do not have significant operations research knowledge could choose the best option by paying attention to the dimensions of the problem complexity.
Cyclical Evolution of Emerging Technology Innovation Network from a Temporal Network Perspective
Authors: Liu Yaqin , Chen Yunsi , He Qing , Yu Qian
Published: February 2023

With the cyclical development of emerging technologies, in reality, the evolution dynamics of their innovation networks will inevitably show obvious time attributes. Numerous network analyses of real complex systems usually focus on static networks; however, it is difficult to describe that most real networks undergo topological evolutions over time. Temporal networks, which incorporate time attributes into traditional static network models, can more accurately depict the temporal features of network evolution. Here, we introduced the time attribute of the life cycle of emerging technology into the evolution dynamics of its innovation network, constructed an emerging technology temporal innovation network from a temporal network perspective, and established its evolution model in combination with the life cycle and key attributes of emerging technology. Based on this model, we took 5G technology as an example to conduct network evolution simulation, verified the rationality of the above model building, and analyzed the cyclical evolution dynamics of this network in various topological structures. The results show that the life cycle of emerging technology, as well as multiple knowledge attributes based on the key attributes of emerging technology, are important factors that affect network evolution by acting on node behaviors. Within this study, we provide a more realistic framework to describe the internal mechanism of the cyclical evolution of emerging technology innovation network, which can extend the research on innovation network evolution from the single topological dynamics to the topological–temporal dynamics containing time attributes and enrich the research dimensions of innovation network evolution from the perspective of temporal evolution.
Thesium hispidifructum (Santalaceae), a New Hispidulous Species from Limpopo, South Africa and Notes on Enigmatic T. celatum
Authors: Lombard Natasha , Le Roux M. Marianne
Published: February 2023

Two shrub-like Thesium species (subgenus Psilothesium) from the Limpopo and North West Provinces in South Africa are treated. Using morphological information from the literature, herbarium material (including types) and geographic information, specimens of the little-known T. celatum N.E.Br. and a new species, T. hispidifructum N.Lombard and M.M.leRoux sp. nov., are treated. A first comprehensive description of the Waterberg–Magaliesberg endemic, T. celatum, is provided along with diagnostic characters to distinguish it from its morphologically most similar-looking species, T. burchellii A.W.Hill. It has hitherto been classified as data deficient due to taxonomic reasons by the International Union for Nature Conservation (IUCN) but a status of Vulnerable is suggested. Thesium hispidifructum is recognised for the first time here and is endemic to Blouberg and Mount Letsjume. It is morphologically most similar to T. disparile N.E.Br. Its name was chosen with reference to its hispidulous to hispid indumentum covering the entire plant including the outside of the flowers and fruit. A threat status of vulnerable is proposed. Treatments of both species include detailed morphological descriptions, information on their distribution and habitat, comparisons and an identification key with morphologically similar species and photo plates.
Epiglottis Cartilage, Costal Cartilage, and Intervertebral Disc Cartilage as Alternative Materials in the Postmortem Diagnosis of Methanol Poisoning
Authors: Tomsia Marcin , Chełmecka Elżbieta , Głaz Małgorzata , Nowicka Joanna
Published: February 2023

Alternative materials for postmortem diagnosis in the case of fatal poisonings are much needed when standard materials, such as blood and urine, are unavailable. The study presents a case of fatal mass methanol intoxication resulting from industrial alcohol consumption. The study aimed to determine methanol and formic acid concentrations in epiglottis cartilage, costal cartilage, and intervertebral disc cartilage and to analyze the correlation between their concentrations in cartilage tissues and the femoral blood. Methanol and formic acid concentrations in samples collected from 17 individuals (n = 17) were estimated using gas chromatography with flame ionization detection (GC-FID). Methanol concentration in the costal cartilage correlated with its concentration in the femoral blood (r = 0.871). Similar correlations were found for epiglottis cartilage (r = 0.822) and intervertebral disc cartilage (r = 0.892). Formic acid concentration in the blood correlated only with its concentration in urine (r = 0.784) and the epiglottis (r = 0.538). Cartilage tissue could serve as an alternative material for methanol analyses in postmortem studies. Formic acid, a methanol metabolite, does not meet the requirements for its presence determination in cartilage tissues.
The Response of Purslane (Portulaca oleracea) to Soil-Added Pb: Is It Suitable as a Potential Phytoremediation Species?
Authors: Thalassinos Georgios , Petropoulos Spyridon A. , Antoniadis Vasileios
Published: February 2023

Soils with high lead (Pb) levels can be decontaminated with the use of tolerant plants. Their effectiveness may be increased with added soil N due to boosted plant vigor, but such an agronomic practice has not been widely reported so far. In this work, purslane (Portulaca oleracea) was tested in a pot experiment as a potential phytoremediation species using soil spiked with Pb at doses of 0, 150, 300, 600, and 900 mg kg−1 (referred to as Pb(0), Pb(150), Pb(300), Pb(600), and Pb(900), respectively) with added N (referred to as N(1); at 300 kg N ha−1) and without added N (N(0)). We found that added Pb did not cause any adverse effects on plant growth (height, and aerial and root dry biomass) and physiological parameters, which were boosted with added N. Lead plant concentration and uptake significantly increased with added N, a finding that confirms our hypothesis. The number of necessary harvests of purslane in order to reduce soil Pb to half its initial concentration was also calculated and found to decrease with added N, being 131 at Pb(900)N(1). Although results indicate the potential of purslane as a phytoremediation species, further research is needed under real field conditions.
Generic Modification of Gravity, Late Time Acceleration and Hubble Tension
Authors: Gangopadhyay Mayukh R. , Pacif Shibesh K. Jas , Sami Mohammad , Sharma Mohit K.
Published: February 2023

We consider a scenario of large-scale modification of gravity that does not invoke extra degrees of freedom, but includes coupling between baryonic matter and dark matter in the Einstein frame. The total matter energy density follows the standard conservation, and evolution has the character of deceleration in this frame. The model exhibits interesting features in the Jordan frame realised by virtue of a disformal transformation where individual matter components adhere to standard conservation but gravity is modified. A generic parametrization of disformal transformation leaves thermal history intact and gives rise to late time acceleration in the Jordan frame, which necessarily includes phantom crossing, which, in the standard framework, can be realised using at least two scalar fields. This scenario is embodied by two distinguished features, namely, acceleration in the Jordan frame and deceleration in the Einstein frame, and the possibility of resolution of the Hubble tension thanks to the emergence of the phantom phase at late times.
The MOVING GROUND Project: A Nature-Positive Case Study
Authors: Anastasopoulos Nicholas , Iliaskou Penelope , Nestora Mariela
Published: February 2023

This paper is a report on the year-long MOVING GROUND project (MG), initiated by the Isadora and Raymond Duncan Dance Research Center (DDRC). The Duncan Dance Research Center sets out to address climate change issues interweaving the social, physical, and artistic spheres by introducing the concept of a garden both literally and metaphorically to inspire the artistic community and shift mindsets of the local community. By a gradual transformation of its grounds, infrastructure, and social fabric, the long-term goal of the DDRC is to function as a tangible model that can be experienced and replicated as a whole or in parts in the city or elsewhere. The paper discusses the goals, methodologies and strategies introduced during the project aiming towards the regenerative transformation of the institution that drew inspiration from permaculture principles, nature-based solutions and a net-positive design perspective. The paper also discusses the novel experimentation of applying permaculture principles to artistic creation and practices. The paper concludes with a reflection of the outcomes and an assessment of the goals it set out to achieve.
Enhanced Viral Metagenomics with Lazypipe 2
Authors: Plyusnin Ilya , Vapalahti Olli , Sironen Tarja , Kant Ravi , Smura Teemu
Published: February 2023

Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.
Recombinant Protein Vaccines Formulated with Enantio-Specific Cationic Lipid R-DOTAP Induce Protective Cellular and Antibody-Mediated Immune Responses in Mice
Authors: Gandhapudi Siva K. , Shi Hua , Ward Martin R. , Bush John Peyton , Avdiushko Margarita , Sundarapandiyan Karuna , Wood Lauren V. , Dorrani Mania , Fatima Afsheen , Dervan Joe , Bedu-Addo Frank , Conn Greg , Ross Ted M. , Woodward Jerold G.
Published: February 2023

Adjuvants are essential components of subunit vaccines added to enhance immune responses to antigens through immunomodulation. Very few adjuvants have been approved for human use by regulatory agencies due to safety concerns. Current subunit vaccine adjuvants approved for human use are very effective in promoting humoral immune responses but are less effective at promoting T-cell immunity. In this study, we evaluated a novel pure enantio-specific cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (R-DOTAP) as an immunomodulator for subunit vaccines capable of inducing both humoral- and cellular-mediated immunity. Using recombinant protein antigens derived from SARS-CoV2 spike or novel computationally optimized broadly reactive influenza antigen (COBRA) proteins, we demonstrated that R-DOTAP nanoparticles promoted strong cellular- and antibody-mediated immune responses in both monovalent and bivalent vaccines. R-DOTAP-based vaccines induced antigen-specific and polyfunctional CD8+ and CD4+ effector T cells and memory T cells, respectively. Antibody responses induced by R-DOTAP showed a balanced Th1/Th2 type immunity, neutralizing activity and protection of mice from challenge with live SARS-CoV2 or influenza viruses. R-DOTAP also facilitated significant dose sparing of the vaccine antigens. These studies demonstrate that R-DOTAP is an excellent immune stimulator for the production of next-generation subunit vaccines containing multiple recombinant proteins.
The Landscape of Expressed Chimeric Transcripts in the Blood of Severe COVID-19 Infected Patients
Authors: Mukherjee Sunanda Biswas , Detroja Rajesh , Mukherjee Sumit , Frenkel-Morgenstern Milana
Published: February 2023

The ongoing COVID-19 pandemic caused by SARS-CoV-2 infections has quickly developed into a global public health threat. COVID-19 patients show distinct clinical features, and in some cases, during the severe stage of the condition, the disease severity leads to an acute respiratory disorder. In spite of several pieces of research in this area, the molecular mechanisms behind the development of disease severity are still not clearly understood. Recent studies demonstrated that SARS-CoV-2 alters the host cell splicing and transcriptional response to overcome the host immune response that provides the virus with favorable conditions to replicate efficiently within the host cells. In several disease conditions, aberrant splicing could lead to the development of novel chimeric transcripts that could promote the functional alternations of the cell. As severe SARS-CoV-2 infection was reported to cause abnormal splicing in the infected cells, we could expect the generation and expression of novel chimeric transcripts. However, no study so far has attempted to check whether novel chimeric transcripts are expressed in severe SARS-CoV-2 infections. In this study, we analyzed several publicly available blood transcriptome datasets of severe COVID-19, mild COVID-19, other severe respiratory viral infected patients, and healthy individuals. We identified 424 severe COVID-19 -specific chimeric transcripts, 42 of which were recurrent. Further, we detected 189 chimeric transcripts common to severe COVID-19 and multiple severe respiratory viral infections. Pathway and gene enrichment analysis of the parental genes of these two subsets of chimeric transcripts reveals that these are potentially involved in immune-related processes, interferon signaling, and inflammatory responses, which signify their potential association with immune dysfunction leading to the development of disease severity. Our study provides the first detailed expression landscape of chimeric transcripts in severe COVID-19 and other severe respiratory viral infections.
Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds
Authors: Vereecke Nick , Woźniak Aleksandra , Pauwels Marthe , Coppens Sieglinde , Nauwynck Hans , Cybulski Piotr , Theuns Sebastiaan , Stadejek Tomasz
Published: February 2023

Influenza A virus (IAV) is a single-stranded, negative-sense RNA virus and a common cause of seasonal flu in humans. Its genome comprises eight RNA segments that facilitate reassortment, resulting in a great variety of IAV strains. To study these processes, the genetic code of each segment should be unraveled. Fortunately, new third-generation sequencing approaches allow for cost-efficient sequencing of IAV segments. Sequencing success depends on various factors, including proper sample storage and processing. Hence, this work focused on the effect of storage of oral fluids and swIAV sequencing. Oral fluids (n = 13) from 2017 were stored at −22 °C and later transferred to −80 °C. Other samples (n = 21) were immediately stored at −80 °C. A reverse transcription quantitative PCR (RT-qPCR) pre- and post-storage was conducted to assess IAV viral loads. Next, samples were subjected to two IAV long-read nanopore sequencing methods to evaluate success in this complex matrix. A significant storage-associated loss of swIAV loads was observed. Still, a total of 17 complete and 6 near-complete Polish swIAV genomes were obtained. Genotype T, (H1avN2, seven herds), P (H1N1pdm09, two herds), U (H1avN1, three herds), and A (H1avN1, 1 herd) were circulated on Polish farms. In conclusion, oral fluids can be used for long-read swIAV sequencing when considering appropriate storage and segment amplification protocols, which allows us to monitor swIAV in an animal-friendly and cost-efficient manner.
Ecological, Genetic, and Phylogenetic Aspects of YFV 2017–2019 Spread in Rio de Janeiro State
Authors: Ribeiro Ieda Pereira , Delatorre Edson , de Abreu Filipe Vieira Santos , dos Santos Alexandre Araújo Cunha , Furtado Nathália Dias , Ferreira-de-Brito Anielly , de Pina-Costa Anielle , Neves Maycon Sebastião Alberto Santos , de Castro Márcia Gonçalves , Motta Monique de Albuquerque , Brasil Patricia , Lourenço-de-Oliveira Ricardo , Bonaldo Myrna Cristina
Published: February 2023

In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2016. Aiming to elucidate the molecular and phylogenetic aspects of YFV spread on a local scale, we generated 43 new YFV genomes sampled from humans, non-human primates (NHP), and primarily, mosquitoes from highly heterogenic areas in 15 localities from Rio de Janeiro (RJ) state during the YFV 2016–2019 outbreak in southeast Brazil. Our analysis revealed that the genetic diversity and spatial distribution of the sylvatic transmission of YFV in RJ originated from at least two introductions and followed two chains of dissemination, here named the YFV RJ-I and YFV RJ-II clades. They moved with similar dispersal speeds from the north to the south of the RJ state in parallel directions, separated by the Serra do Mar Mountain chain, with YFV RJ-I invading the north coast of São Paulo state. The YFV RJ-I clade showed a more significant heterogeneity across the entire polyprotein. The YFV RJ-II clade, with only two amino acid polymorphisms, mapped at NS1 (I1086V), present only in mosquitoes at the same locality and NS4A (I2176V), shared by all YFV clade RJ-II, suggests a recent clustering of YFV isolates collected from different hosts. Our analyses strengthen the role of surveillance, genomic analyses of YVF isolated from other hosts, and environmental studies into the strategies to forecast, control, and prevent yellow fever outbreaks.
Longitudinal IgA and IgG Response, and ACE2 Binding Blockade, to Full-Length SARS-CoV-2 Spike Protein Variants in a Population of Black PLWH Vaccinated with ChAdOx1 nCoV-19
Authors: Smith Muneerah , Kwatra Gaurav , Izu Alane , Nel Andrew , Cutland Clare , Ahmed Khatja , Baillie Vicky , Barnabas Shaun , Bhorat Qasim , Briner Carmen , Lazarus Erica , Dheda Keertan , Fairlie Lee , Koen Anthonet , Madhi Shabir , Blackburn Jonathan M.
Published: February 2023

Vaccines against SARS-CoV-2 have been pivotal in overcoming the COVID-19 pandemic yet understanding the subsequent outcomes and immunological effects remain crucial, especially for at-risk groups e.g., people living with human immunodeficiency virus (HIV) (PLWH). In this study we report the longitudinal IgA and IgG antibody titers, as well as antibody-mediated angiotensin converting enzyme 2 (ACE2) binding blockade, against the SARS-CoV-2 spike (S) proteins after 1 and 2 doses of the ChAdOx1 nCoV-19 vaccine in a population of Black PLWH. Here, we report that PLWH (N = 103) did not produce an anti-S IgA response after infection or vaccination, however, anti-S IgG was detected in response to vaccination and infection, with the highest level detected for infected vaccinated participants. The anti-IgG and ACE2 blockade assays revealed that both vaccination and infection resulted in IgG production, however, only vaccination resulted in a moderate increase in ACE2 binding blockade to the ancestral S protein. Vaccination with a previous infection results in the greatest anti-S IgG and ACE2 blockade for the ancestral S protein. In conclusion, PLWH produce an anti-S IgG response to the ChAdOx1 nCoV-19 vaccine and/or infection, and ChAdOx1 nCoV-19 vaccination with a previous infection produced more neutralizing antibodies than vaccination alone.
Pro-Viral and Anti-Viral Roles of the RNA-Binding Protein G3BP1
Authors: Jayabalan Aravinth Kumar , Griffin Diane E. , Leung Anthony K. L.
Published: February 2023

Viruses depend on host cellular resources to replicate. Interaction between viral and host proteins is essential for the pathogens to ward off immune responses as well as for virus propagation within the infected cells. While different viruses employ unique strategies to interact with diverse sets of host proteins, the multifunctional RNA-binding protein G3BP1 is one of the common targets for many viruses. G3BP1 controls several key cellular processes, including mRNA stability, translation, and immune responses. G3BP1 also serves as the central hub for the protein–protein and protein–RNA interactions within a class of biomolecular condensates called stress granules (SGs) during stress conditions, including viral infection. Increasing evidence suggests that viruses utilize distinct strategies to modulate G3BP1 function—either by degradation, sequestration, or redistribution—and control the viral life cycle positively and negatively. In this review, we summarize the pro-viral and anti-viral roles of G3BP1 during infection among different viral families.
Japanese Encephalitis Enzootic and Epidemic Risks across Australia
Authors: Furlong Morgan , Adamu Andrew M. , Hoskins Andrew , Russell Tanya L. , Gummow Bruce , Golchin Maryam , Hickson Roslyn I. , Horwood Paul F.
Published: February 2023

Japanese encephalitis virus (JEV) is an arboviral, encephalitogenic, zoonotic flavivirus characterized by its complex epidemiology whose transmission cycle involves reservoir and amplifying hosts, competent vector species and optimal environmental conditions. Although typically endemic in Asia and parts of the Pacific Islands, unprecedented outbreaks in both humans and domestic pigs in southeastern Australia emphasize the virus’ expanding geographical range. To estimate areas at highest risk of JEV transmission in Australia, ecological niche models of vectors and waterbirds, a sample of piggery coordinates and feral pig population density models were combined using mathematical and geospatial mapping techniques. These results highlight that both coastal and inland regions across the continent are estimated to have varying risks of enzootic and/or epidemic JEV transmission. We recommend increased surveillance of waterbirds, feral pigs and mosquito populations in areas where domestic pigs and human populations are present.
The Prevalence of HPV in Oral Cavity Squamous Cell Carcinoma
Authors: Katirachi Seyed Keybud , Grønlund Mathias Peter , Jakobsen Kathrine Kronberg , Grønhøj Christian , von Buchwald Christian
Published: February 2023

Human papillomavirus (HPV) is an important risk factor in a subset of head and neck squamous cell carcinomas (HNSCC), but the association with oral cavity squamous cell carcinomas (OCSCC) remains controversial. This study aimed to identify the prevalence of HPV infection in OCSCC. A systematic search on PubMed and EMBASE was performed, including articles assessing the prevalence of HPV-positive (HPV+) OCSCC published from January 2017 to December 2022. OCSCC was considered HPV+ by the detection of HPV DNA, HPV RNA, and/or p16 overexpression in the tumor mass. A meta-analysis was made determining the overall HPV+ OCSCC prevalence. We included 31 studies comprising 5007 patients from 24 countries. The study size ranged from 17 to 940 patients. The HPV+ OCSCC proportion variated widely and ranged from 0% to 37%. Tumors in the tongue were the predominant sublocation for HPV in the oral cavity. The meta-analysis revealed that the overall HPV+ OCSCC prevalence is 6% (95% CI; 3–10%), and only one study found HPV and OCSCC significantly associated. Thus, HPV may not be a necessary or a strong risk factor in OCSCC oncogenesis, and the possibility of a site misclassification of a mobile tongue with the root of the tongue cannot be excluded.
HoBi-like Pestivirus Is Highly Prevalent in Cattle Herds in the Amazon Region (Northern Brazil)
Authors: Baumbach Leticia F. , Mósena Ana Cristina S. , Alves Raquel S. , Camargo Laura J. , Olegário Juliana C. , Lobraico Leonardo R. , Costa João Marcos N. , Borba Mauro R. , Bauermann Fernando V. , Weber Matheus N. , Canal Cláudio W.
Published: February 2023

Pestiviruses are globally distributed and cause substantial economic losses to the cattle industry. In Brazil, the country with the world’s largest cattle population, pestivirus infections are well described in some regions, such as in the south, where a high frequency of BVDV-2 is described and contrasts with the high prevalence of HoBi-like pestivirus (HoBiPeV) in the northeast. However, there is a lack of information about pestiviruses in the Amazon Region, in northern Brazil, with a cattle population estimated at 55.7 million head, which has a significant impact on the international livestock market. Therefore, this study investigated the seroprevalence and genetic variability of ruminant pestiviruses in 944 bovine serum samples from four states in northern Brazil: Pará (PA), Amapá (AP), Roraima (RR), and Amazonas (AM). Our results showed that 45.4% of the samples were seropositive (19.8% for BVDV-1, 14.1% for BVDV-2, and 20.9% for HoBiPeV). All samples were tested by RT–qPCR, and three were positive and classified as HoBiPeV in a phylogenetic analysis. These serological and molecular results contrast with those from other regions of the world, suggesting that the northern Brazilian states have a high prevalence of all bovine pestiviruses including HoBiPeV.
One-Year Post-Vaccination Longitudinal Follow-Up of Quantitative SARS-CoV-2 Anti-Spike Total Antibodies in Health Care Professionals and Evaluation of Correlation with Surrogate Neutralization Test
Authors: Tuyji Tok Yesim , Can Sarinoglu Rabia , Ordekci Seyhan , Yilmaz Serife , Ozcolpan Gunes , Bayram Aysen , Nohut Okan Kadir , Kocer Ipek , Hasdemir Ufuk , Kuskucu Mert Ahmet , Konukoglu Dildar , Gozalan Aysegul , Midilli Kenan , Celik Gulden
Published: February 2023

Numerous vaccines have been generated to decrease the morbidity and mortality of COVID-19. This study aims to evaluate the immunogenicity of the heterologous boosts by BioNTech against homologous boosts by CoronaVac at three-month intervals in two health care worker (HCW) cohorts, with or without prior COVID-19, for one year post-vaccination. This is a prospective cohort study in which the humoral responses of 386 HCWs were followed-up longitudinally in six main groups according to their previous COVID-19 exposure and vaccination status. Anti-SARS-CoV-2 spike-RBD total antibody levels were measured and SARS-CoV-2 neutralization antibody (NAbs) responses against the ancestral Wuhan and the Omicron variant were evaluated comparatively using international standard serum for Wuhan and Omicron, as well as with the aid of a conversion tool. The anti-SARS-CoV-2 spike-RBD total Ab and Nab difference between with and without prior COVID-19, three months after two-dose primary vaccination with CoronaVac, was statistically significant (p = 0.001). In the subsequent follow-ups, this difference was not observed between the groups. Those previously infected (PI) and non-previously infected (NPI) groups receiving BioNTech as the third dose had higher anti-SARS-CoV-2 spike total Ab levels (14.2-fold and 17.4-fold, respectively, p = 0.001) and Nab responses (against Wuhan and Omicron) than those receiving CoronaVac. Ab responses after booster vaccination decreased significantly in all groups at the ninth-month follow-up (p < 0.05); however, Abs were still higher in all booster received groups than that in the primary vaccination. Abs were above the protective level at the twelfth-month measurement in the entire of the second BioNTech received group as the fourth dose of vaccination. In the one-year follow-up period, the increased incidence of COVID-19 in the groups vaccinated with two or three doses of CoronaVac compared with the groups vaccinated with BioNTech as a booster suggested that continuing the heterologous CoronaVac/BioNTech vaccination, revised according to current SARS-CoV-2 variants and with at least a six-month interval booster would be an effective and safe strategy for protection against COVID-19, particularly in health care workers.
Safety Following COVID-19 Booster Vaccine with BNT162b2 Compared to mRNA-1273 in Solid Cancer Patients Previously Vaccinated with ChAdOx1 or CoronaVac
Authors: Wanchaijiraboon Passakorn , Sainamthip Panot , Teeyapun Nattaya , Luangdilok Sutima , Poovorawan Yong , Wanlapakorn Nasamon , Tanasanvimon Suebpong , Sriuranpong Virote , Susiriwatananont Thiti , Zungsontiporn Nicha , Pakvisal Nussara
Published: February 2023

Safety data following the COVID-19 booster mRNA vaccine in solid cancer patients are scarce. We prospectively evaluated adverse events after a booster dose of the BNT162b2 vaccine as compared to the mRNA-1273 vaccine in solid malignancy patients who had previously received two doses of ChAdOx1 or heterogenous CoronaVac/ChAdOx1. Data regarding solicited and unsolicited adverse events were collected using questionnaires. The primary endpoint was the difference in incidence and severity of adverse events between BNT162b2 and mRNA-1273 vaccines. A total of 370 subjects were enrolled, including 172 (47%) and 198 (54%) patients receiving booster doses of BNT162b2 and mRNA-1273 vaccines, respectively. The overall incidence of adverse events in the two groups was comparable (BNT162b2 vs. mRNA-1273; 63% vs. 66%, p = 0.6). There was no significant difference in severity, and the majority of adverse events reported were classed as mild to moderate. Tenderness at the injection site was the only reaction that had a statistically higher reported incidence after the mRNA-1273 vaccine than after the BNT162b2 vaccine (56% vs. 41%, p = 0.003). In conclusion, a booster dose of the mRNA vaccine, either BNT162b2 or mRNA-1273, in solid cancer patients previously vaccinated with ChAdOx1 and CoronaVac appears safe, and no new safety concerns were observed.
Using Dried Blood Spots for a Sero-Surveillance Study of Maternally Derived Antibody against Group B Streptococcus
Authors: Auma Erick , Hall Tom , Chopra Simran , Bilton Sam , Ramkhelawon Laxmee , Amini Fahimah , Calvert Anna , Amirthalingam Gayatri , Jones Christine E. , Andrews Nick , Heath Paul T. , Le Doare Kirsty
Published: February 2023

Vaccination during pregnancy could protect women and their infants from invasive Group B Streptococcus (GBS) disease. To understand if neonatal dried blood spots (DBS) can be used to determine the amount of maternally derived antibody that protects infants against invasive GBS disease, a retrospective case-control study was conducted in England between 1 April 2014 and 30 April 2015. The DBS of cases with invasive GBS disease (n = 61) were matched with healthy controls (n = 125). The haematocrit, DBS storage temperature, freeze-thaw cycle, and paired serum/DBS studies were set up to optimise the antibody assessment. The samples were analysed using a multiplex immunoassay, and the results were assessed using parametric and nonparametric tests. Antibody concentrations were stable at haematocrits of up to 50% but declined at 75%. DBS storage at room temperature was stable for three months compared with storage from collection at −20 °C and rapidly degraded thereafter. Total IgG levels measured in DBS and paired serum showed a good correlation (r2 = 0.99). However, due to suboptimal storage conditions, no difference was found in the GBS IgG levels between DBS samples from cases and controls. We have demonstrated a proof of concept that assays utilising DBS for assessing GBS serotype-specific antibodies in infants is viable. This method could be used to facilitate future large sero-correlate studies, but DBS samples must be stored at −20 °C for long term preservation of antibody.
SARS-CoV-2 Antibody Dynamics in Healthcare Workers after mRNA Vaccination
Authors: Dieckhaus Kevin D. , Kim Min-Jung , Shen Jian-Bing , Liang Tina S. , Kleinberg Michael J. , Siedlarz Kristen M. , Banach David B. , Metersky Mark L. , Fuller Rob P. , Mortensen Eric M. , Liang Bruce T.
Published: February 2023

Since the emergence of SARS-CoV-2, maintaining healthcare worker (HCW) health and safety has been fundamental to responding to the global pandemic. Vaccination with mRNA-base vaccines targeting SARS-CoV-2 spike protein has emerged as a key strategy in reducing HCW susceptibility to SARS-CoV-2, however, neutralizing antibody responses subside with time and may be influenced by many variables. We sought to understand the dynamics between vaccine products, prior clinical illness from SARS-CoV-2, and incidence of vaccine-associated adverse reactions on antibody decay over time in HCWs at a university medical center. A cohort of 296 HCWs received standard two-dose vaccination with either bnt162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna) and were evaluated after two, six, and nine months. Subjects were grouped by antibody decay curve into steep antibody decliners gentle decliners. Vaccination with mRNA-1273 led to more sustained antibody responses compared to bnt162b2. Subjects experiencing vaccine-associated symptoms were more likely to experience a more prolonged neutralizing antibody response. Subjects with clinical SARS-CoV-2 infection prior to vaccination were more likely to experience vaccination-associated symptoms after first vaccination and were more likely to have a more blunted antibody decay. Understanding factors associated with vaccine efficacy may assist clinicians in determining appropriate vaccine strategies in HCWs.