bluuebunny/crossref_metadata_2025 huggingface dataset:
Ship Graffiti in Horologion of Andronikos Kyrristos, Greece: A Comparative Study and New Evidence
Authors: Panou Evangelia , Kaminari Agathi Anthoula , Tsairis Georgios , Alexopoulou Athina Georgia
Published: October 2022

The paper contributes new information about the Horologion of Andronikos Kyrristos of the Roman Agora of Athens, Greece and its continuous presence in Athens from antiquity until now. The monument is of cultural, historical and astronomical importance. It has undergone conservation work and non-destructive documentation which contribute to its sustainability. The spectral imaging technique, which allows the acquisition of high-resolution images, was applied on the stone surfaces of the monument. The acquisition of images in the visible and infrared regions, combined with the digital tracing reproduction of the graffiti and image processing, is used for the first time in this particularly interesting case study of the aforementioned monument, of which a complete description is provided. New evidence with a clearer recording of the vessels already mentioned in the literature, as well as the detection of new historical data and graffiti, is discussed in comparison with the results of previous studies.
Toward a Comprehensive Framework of Social Innovation for Climate Neutrality: A Systematic Literature Review from Business/Production, Public Policy, Environmental Sciences, Energy, Sustainability and Related Fields
Authors: Bresciani Sabrina , Rizzo Francesca , Deserti Alessandro
Published: October 2022

Social Innovation (SI) is considered a key lever for supporting climate action and decarbonization. In addition to the adoption of technological innovations, novel social practices can lead to the reconfiguration of socio-technical systems toward more democratic energy transitions and heightened civic participation for climate action. Several frameworks and cases of social innovation for climate neutrality are described in the academic literature; however, this rich body of knowledge is scattered across different fields and the actual relevance of social innovation for climate is rarely measured. A core challenge remains regarding the systematic assessment of social innovation’s contribution to decarbonization. With the aim of developing a comprehensive framework for potentially assessing social innovations, the extant literature is mapped and the following key dimensions of social innovation for climate neutrality are derived: context, input (or resources), social innovation activities (capacity building, types of SI initiatives and scaling), and results (immediate outputs, medium-term outcomes, long-term impact toward wellbeing). The framework has both theoretical and practical relevance: it provides a structured pathway of social innovation mechanisms and related assessment categories, which can be deployed showing evidence of social innovation effects, gaining insights for actions’ improvements, as well as informing policy-making.
Status and Trends of Membrane Technology for Wastewater Treatment: A Patent Analysis
Authors: Cerveira Graziela Salvan , Magalhães Jorge Lima de , Antunes Adelaide Maria de Souza
Published: October 2022

Global access to clean water and sanitation has been broadly discussed in the context of the Sustainable Development Goals adopted by the United Nations. In this context, membrane technology has been increasingly applied with great success in wastewater treatment. Considering the relevance of patent information for understanding the current status and future trends of technologies, the patent filings on membrane technology for wastewater treatment in the period from 2011 to 2019 were analyzed. This study comprised a global analysis, aimed at determining the most general aspects, and a qualitative analysis, which consisted of a careful reading of the documents to assess technological statuses and trends. From a total of 7303 patent documents found on the topic, 488 documents were selected for the qualitative analysis. China, Japan and the United States play a leading role in the development of these technologies. Companies constitute the vast majority of the applicants. The focus of the inventions turned out to be: equipment, membranes, customized equipment/processes for specific wastewaters, fouling control and cleaning, combinations of technologies and sustainability. Finally, enhancements in the operational performance of the membrane separation equipment and the development of membrane materials with increased water flow and fouling resistance are found to be key factors to broaden the application of membrane separation technology in wastewater treatment.
The Impact of Urbanization Level on Urban–Rural Income Gap in China Based on Spatial Econometric Model
Authors: Zhao Xiaomeng , Liu Lin
Published: October 2022

With the rapid development of China’s economy, urbanization is gradually accelerating, but the income gap between urban and rural areas is growing, which may constrain economic development. To test the impact of urbanization on the urban–rural income gap, this paper uses panel data of 31 provinces (cities/autonomous regions) in China from 2007 to 2018, and combines ArcGIS technology to construct Spatial Dubin Model. This paper finds that the increase in urbanization level in China can significantly reduce the urban–rural income gap. The mediating effects model further shows that the increased level of urbanization in China promotes the flow of factors, which helps the flow of capital and advanced technology into the countryside and increases productivity. It also promotes the transfer of a large amount of surplus labor to the tertiary sector, adjusting the industrial structure and increasing the income of peasants moving to the city. In addition, the development of urbanization in China can lead to the construction of public education, improving the conditions and quality of education and teaching, and increasing the possibilities for farmers to earn high incomes. As a result, the urban–rural income gap in China has been narrowed. The findings of this paper are useful for understanding the underlying mechanisms in the level of urbanization and the urban–rural income gap in China. It provides policy insights for accelerating China’s new urbanization process and promoting the coordinated development of China’s urban and rural regions.
Analysis of Polycyclic Aromatic Hydrocarbons (PAHs) Sources and Vertical Distribution in Soils of the Age-Diverse Brownfields of Southern Poland Using Positive Matrix Factorisation and Data Mining Model
Authors: Ciarkowska Krystyna , de Carvalho Messias , Gambus Florian
Published: October 2022

In this study, we aimed at understanding a relation between PAH accumulation in the soils of brownfields that differed in origin (i.e., waste after coal mining, power plant, zinc–lead- or iron-ore processing) and age (400 years old to present). PAH contents were determined after their extraction with 2-propanol using a gas chromatograph (GC) equipped with a flame ionisation detector (FID) and a FactorFour VF-5MS capillary column. Sources of PAHs were identified using positive matrix factorisation (PMF). In regard to the relevance of the variables that helped explain the PAH accumulation, a random forest (RF) method was used. PMF analysis highlighted the connection of PAH sources with the industrial activity performed in the area. PAH concentrations increased with the age of tailings, but always exceeded the threshold-effect levels, indicating their potential to cause harm to humans. The RF method showed that for 2–3-ring PAHs the most important factor was the carbon content followed by clay, site, depth, pH, and then nitrogen, while for other PAHs, only the N content and depth exceeded 50% importance. PAHs’ vertical distributions reflected the history and the time passing from the brownfield site formation. Severe contamination of the brownfield soils indicates the necessity for remediation measures, especially where there are plans to build on these areas.
The Mediating and Moderating Effect of Organizational Resilience on Competitive Advantage: Evidence from Chinese Companies
Authors: Wang Juan , Chen Ruijun , Zhang Shuang
Published: October 2022

Enhancing organizational resilience is an important way for enterprises to achieve sustained competitive advantage. Based on dynamic capability theory, organizational learning theory, and resource-based theory, this study constructs a theoretical model of organizational resilience and sustained competitive advantage with organizational learning as the mediating variable and environmental dynamism as the moderating variable. This study is based on questionnaire research data from 462 Chinese companies in selected regions as the research sample for empirical testing, and the results show that organizational resilience helps Chinese companies to gain sustainable competitive advantage; organizational learning plays a mediating role between organizational resilience and sustainable competitive advantage; and environmental dynamics has a positive moderating role between organizational resilience and organizational learning, and can positively regulate the path of organizational resilience affecting sustainable competitive advantage through organizational learning. In view of this, we propose practical insights for Chinese companies on three levels: motivating mechanisms for organizational resilience, shaping a good learning environment, and paying attention to the dynamics of the environment.
Remarks on Fractal-Fractional Malkus Waterwheel Model with Computational Analysis
Authors: Guran Liliana , Akgül Esra Karataş , Akgül Ali , Bota Monica-Felicia
Published: October 2022

In this paper, we investigate the fractal-fractional Malkus Waterwheel model in detail. We discuss the existence and uniqueness of a solution of the fractal-fractional model using the fixed point technique. We apply a very effective method to obtain the solutions of the model. We prove with numerical simulations the accuracy of the proposed method. We put in evidence the effects of the fractional order and the fractal dimension for a symmetric Malkus Waterwheel model.
MULBER: Effective Android Malware Clustering Using Evolutionary Feature Selection and Mahalanobis Distance Metric
Authors: Duraisamy Soundrapandian Pradeepkumar , Subbiah Geetha
Published: October 2022

Symmetric and asymmetric patterns are fascinating phenomena that show a level of co-existence in mobile application behavior analyses. For example, static phenomena, such as information sharing through collaboration with known apps, is a good example of a symmetric model of communication, and app collusion, where apps collaborate dynamically with unknown malware apps, is an example of a serious threat with an asymmetric pattern. The symmetric nature of app collaboration can become vulnerable when a vulnerability called PendingIntent is exchanged during Inter-Component Communication (ICC). The PendingIntent (PI) vulnerability enables a flexible software model, where the PendingIntent creator app can temporarily share its own permissions and identity with the PendingIntent receiving app. The PendingIntent vulnerability does not require approval from the device user or Android OS to share the permissions and identity with other apps. This is called a PI leak, which can lead to malware attacks such as privilege escalation and component hijacking attacks. This vulnerability in the symmetric behavior of an application without validating an app’s privileges dynamically leads to the asymmetric phenomena that can damage the robustness of an entire system. In this paper, we propose MULBER, a lightweight machine learning method for the detection of Android malware communications that enables a cybersecurity system to analyze multiple patterns and learn from them to help prevent similar attacks and respond to changing behavior. MULBER can help cybersecurity teams to be more proactive in preventing dynamic PI-based communication threats and responding to active attacks in real time. MULBER performs a static binary analysis on the APK file and gathers approximately 10,755 features, reducing it to 42 key features by grouping the permissions under the above-mentioned four categories. Finally, MULBER learns from these multivariate features using evolutionary feature selection and the Mahalanobis distance metric and classifies them as either benign or malware apps. In an evaluation of 22,638 malware samples from recent Android APK malware databases such as Drebin and CICMalDroid-2020, MULBER outperformed others by clustering applications based on the Mahalanobis distance metric and detected 95.69% of malware with few false alarms and the explanations provided for each detection revealed the relevant properties of the detected malware.
Reproducing Kernel Hilbert Space Approach to Multiresponse Smoothing Spline Regression Function
Authors: Lestari Budi , Chamidah Nur , Aydin Dursun , Yilmaz Ersin
Published: October 2022

In statistical analyses, especially those using a multiresponse regression model approach, a mathematical model that describes a functional relationship between more than one response variables and one or more predictor variables is often involved. The relationship between these variables is expressed by a regression function. In the multiresponse nonparametric regression (MNR) model that is part of the multiresponse regression model, estimating the regression function becomes the main problem, as there is a correlation between the responses such that it is necessary to include a symmetric weight matrix into a penalized weighted least square (PWLS) optimization during the estimation process. This is, of course, very complicated mathematically. In this study, to estimate the regression function of the MNR model, we developed a PWLS optimization method for the MNR model proposed by a previous researcher, and used a reproducing kernel Hilbert space (RKHS) approach based on a smoothing spline to obtain the solution to the developed PWLS optimization. Additionally, we determined the symmetric weight matrix and optimal smoothing parameter, and investigated the consistency of the regression function estimator. We provide an illustration of the effects of the smoothing parameters for the estimation results using simulation data. In the future, the theory generated from this study can be developed within the scope of statistical inference, especially for the purpose of testing hypotheses involving multiresponse nonparametric regression models and multiresponse semiparametric regression models, and can be used to estimate the nonparametric component of a multiresponse semiparametric regression model used to model Indonesian toddlers’ standard growth charts.
Background Independence and Gauge Invariance in General Relativity Part 2—Covariant Quantum Gravity
Authors: Tessarotto Massimo , Cremaschini Claudio
Published: October 2022

Background independence is often being claimed as the characteristic property of several current and past models of Quantum Gravity. In actual fact, such a notion has a wider connotation and must be rooted into the validity of the general covariance principle, demanding its logical connection with the notions of manifest covariance and (quantum) gauge invariance. In fact, as we intend to show here, it involves (a) the existence of a well-defined, albeit arbitrary, classical background space-time; and (b) the suitable realization of a dynamical equation for the related background metric field tensor, referred to as quantum-modified Einstein tensor field equation, which actually determines it in a suitable functional setting. Remarkably, it is proved that in the context of the theory of Covariant Quantum Gravity (CQG-theory), recently developed by Cremaschini and Tessarotto (2015–2022), background independence implies that such an equation “emerges” rigorously from the same CQG-theory. This follows in terms of a stochastic quantum expectation value evaluated with respect to the corresponding characteristic quantum PDE. It is shown that an analogous emergence property applies also to the background metric field tensor in terms of stochastic fluctuations of the corresponding underlying quantum tensor of gravitational field. These results warrant the consistent validity of background independence for the prescription of the space-time metric tensor in CQG-theory.
A Transcriptome- and Interactome-Based Analysis Identifies Repurposable Drugs for Human Breast Cancer Subtypes
Authors: Conte Federica , Sibilio Pasquale , Fiscon Giulia , Paci Paola
Published: October 2022

Breast cancer (BC) is a heterogeneous and complex disease characterized by different subtypes with distinct morphologies and clinical implications and for which new and effective treatment options are urgently demanded. The computational approaches recently developed for drug repurposing provide a very promising opportunity to offer tools that efficiently screen potential novel medical indications for various drugs that are already approved and used in clinical practice. Here, we started with disease-associated genes that were identified through a transcriptome-based analysis, which we used to predict potential repurposable drugs for various breast cancer subtypes by using an algorithm that we developed for drug repurposing called SAveRUNNER. Our findings were also in silico validated by performing a gene set enrichment analysis, which confirmed that most of the predicted repurposable drugs may have a potential treatment effect against breast cancer pathophenotypes.
Highly Selective Adsorption of 99TcO4−/ReO4− by a Novel Polyamide-Functionalized Polyacrylamide Polymer Material
Authors: Qin Ben , Hu Yanqin , Xie Meiying , Xue Liyan , Liao Chunfa , Yang Fan
Published: October 2022

The treatment of radioactive wastewater is one of the major problems in the current research. With the development of nuclear energy, the efficient removal of 99TcO4− in radioactive wastewater has attracted the attention of countries all over the world. In this study, a novel functional polyamide polymer p-(Amide)-PAM was synthesized by the two-step method. The experimental results show that p-(Amide)-PAM has good adsorptive properties for 99TcO4−/ReO4− and has good selectivity in the nitric acid system. The kinetics of the reaction of p-(Amide)-PAM with 99TcO4−/ReO4− was studied. The results show that p-(Amide)-PAM has a fast adsorption rate for 99TcO4−/ReO4−, the saturated adsorption capacity reaches 346.02 mg/g, and the material has good reusability. This new polyamide-functionalized polyacrylamide polymer material has good application prospects in the removal of 99TcO4− from radioactive wastewater.
Determination of 31 Polycyclic Aromatic Hydrocarbons in Plant Leaves Using Internal Standard Method with Ultrasonic Extraction–Gas Chromatography–Mass Spectrometry
Authors: Yang Ming , Tian Shili , Liu Qingyang , Yang Zheng , Yang Yifan , Shao Peng , Liu Yanju
Published: October 2022

The method for the determination of 16 priority polycyclic aromatic hydrocarbons (PAHs) in plant leaves has been studied extensively, yet the quantitativemethod for measuring non-priority PAHs in plant leaves is limited. A method for the simultaneous determination of 31 polycyclic aromatic hydrocarbons (PAHs) in plant leaves was established using an ultrasonic extraction–gas chromatography–mass spectrometry–internal standard method. The samples of plant leaves were extracted with ultrasonic extraction and purified with solid-phase extraction columns. The PAHs were separated by using gas chromatography–mass spectrometry equipped with a DB-EUPAH capillary column (20 m × 0.18 mm × 0.14 μm) with a selective ion monitoring (SIM) detection mode, and quantified with an internal standard. The method had good linearity in the range of 0.005~1.0 μg/mL with correlation coefficients greater than 0.99, and the method detection limit and maximum quantitative detection limit were in the ranges of 0.2~0.7 μg/kg and 0.8~2.8 μg/kg, respectively. The method was verified with spiked recovery experiments. The average spiked recovery ranged from 71.0% to 97.6% and relative standard deviations (n = 6) were less than 14%. Herein, we established a quantitativemethod for the simultaneous determination of priority and non-priority PAHs in plant leaves using GC–MS. The method is highly sensitive and qualitatively accurate, and it is suitable for the determination of PAHs in plant leaves.
A Review of the Proteomic Profiling of African Viperidae and Elapidae Snake Venoms and Their Antivenom Neutralisation
Authors: Offor Benedict C. , Muller Beric , Piater Lizelle A.
Published: October 2022

Snakebite envenoming is a neglected tropical disease (NTD) that results from the injection of snake venom of a venomous snake into animals and humans. In Africa (mainly in sub-Saharan Africa), over 100,000 envenomings and over 10,000 deaths per annum from snakebite have been reported. Difficulties in snakebite prevention and antivenom treatment are believed to result from a lack of epidemiological data and underestimated figures on snakebite envenoming-related morbidity and mortality. There are species- and genus-specific variations associated with snake venoms in Africa and across the globe. These variations contribute massively to diverse differences in venom toxicity and pathogenicity that can undermine the efficacy of adopted antivenom therapies used in the treatment of snakebite envenoming. There is a need to profile all snake venom proteins of medically important venomous snakes endemic to Africa. This is anticipated to help in the development of safer and more effective antivenoms for the treatment of snakebite envenoming within the continent. In this review, the proteomes of 34 snake venoms from the most medically important snakes in Africa, namely the Viperidae and Elipdae, were extracted from the literature. The toxin families were grouped into dominant, secondary, minor, and others based on the abundance of the protein families in the venom proteomes. The Viperidae venom proteome was dominated by snake venom metalloproteinases (SVMPs–41%), snake venom serine proteases (SVSPs–16%), and phospholipase A2 (PLA2–17%) protein families, while three-finger toxins (3FTxs–66%) and PLA2s (16%) dominated those of the Elapidae. We further review the neutralisation of these snake venoms by selected antivenoms widely used within the African continent. The profiling of African snake venom proteomes will aid in the development of effective antivenom against snakebite envenoming and, additionally, could possibly reveal therapeutic applications of snake venom proteins.
The Middle Eastern Cousin: Comparative Venomics of Daboia palaestinae and Daboia russelii
Authors: Senji Laxme R. R. , Khochare Suyog , Attarde Saurabh , Kaur Navneet , Jaikumar Priyanka , Shaikh Naeem Yusuf , Aharoni Reuven , Primor Naftali , Hawlena Dror , Moran Yehu , Sunagar Kartik
Published: October 2022

Among the medically most important snakes in the world, the species belonging to the genus Daboia have been attributed to the highest number of human envenomings, deaths and disabilities. Given their significant clinical relevance, the venoms of Russell’s vipers (D. russelii and D. siamensis) have been the primary focus of research. In contrast, the composition, activity, ecology and evolution of venom of its congener, the Palestine viper (D. palaestinae), have remained largely understudied. Therefore, to unravel the factors responsible for the enhanced medical relevance of D. russelii in comparison to D. palaestinae, we comparatively evaluated their venom proteomes, biochemical activities, and mortality and morbidity inflicting potentials. Furthermore, the synthesis and regulation of venom in snakes have also remained underinvestigated, and the relative contribution of each venom gland remains unclear. We address this knowledge gap by sequencing the tissue transcriptomes of both venom glands of D. palaestinae, and comparatively evaluating their contribution to the secreted venom concoction. Our findings highlight the disparity in the venom composition, function and toxicities of the two Daboia species. We also show that toxin production is not partitioned between the two venom glands of D. palaestinae.
Dengue Prediction in Latin America Using Machine Learning and the One Health Perspective: A Literature Review
Authors: Cabrera Maritza , Leake Jason , Naranjo-Torres José , Valero Nereida , Cabrera Julio C. , Rodríguez-Morales Alfonso J.
Published: October 2022

Dengue fever is a serious and growing public health problem in Latin America and elsewhere, intensified by climate change and human mobility. This paper reviews the approaches to the epidemiological prediction of dengue fever using the One Health perspective, including an analysis of how Machine Learning techniques have been applied to it and focuses on the risk factors for dengue in Latin America to put the broader environmental considerations into a detailed understanding of the small-scale processes as they affect disease incidence. Determining that many factors can act as predictors for dengue outbreaks, a large-scale comparison of different predictors over larger geographic areas than those currently studied is lacking to determine which predictors are the most effective. In addition, it provides insight into techniques of Machine Learning used for future predictive models, as well as general workflow for Machine Learning projects of dengue fever.
Frame-Dragging in Extrasolar Circumbinary Planetary Systems
Authors: Iorio Lorenzo
Published: October 2022

Extrasolar circumbinary planets are so called because they orbit two stars instead of just one; to date, an increasing number of such planets have been discovered with a variety of techniques. If the orbital frequency of the hosting stellar pair is much higher than the planetary one, the tight stellar binary can be considered as a matter ring current generating its own post-Newtonian stationary gravitomagnetic field through its orbital angular momentum. It affects the orbital motion of a relatively distant planet with Lense-Thirring-type precessional effects which, under certain circumstances, may amount to a significant fraction of the static, gravitoelectric ones, analogous to the well known Einstein perihelion precession of Mercury, depending only on the masses of the system’s bodies. Instead, when the gravitomagnetic field is due solely to the spin of each of the central star(s), the Lense-Thirring shifts are several orders of magnitude smaller than the gravitoelectric ones. In view of the growing interest in the scientific community about the detection of general relativistic effects in exoplanets, the perspectives of finding new scenarios for testing such a further manifestation of general relativity might be deemed worth of further investigations.
Revisiting Papillomavirus Taxonomy: A Proposal for Updating the Current Classification in Line with Evolutionary Evidence
Authors: Van Doorslaer Koenraad
Published: October 2022

Papillomaviruses infect a wide array of animal hosts and are responsible for roughly 5% of all human cancers. Comparative genomics between different virus types belonging to specific taxonomic groupings (e.g., species, and genera) has the potential to illuminate physiological differences between viruses with different biological outcomes. Likewise, extrapolation of features between related viruses can be very powerful but requires a solid foundation supporting the evolutionary relationships between viruses. The current papillomavirus classification system is based on pairwise sequence identity. However, with the advent of metagenomics as facilitated by high-throughput sequencing and molecular tools of enriching circular DNA molecules using rolling circle amplification, there has been a dramatic increase in the described diversity of this viral family. Not surprisingly, this resulted in a dramatic increase in absolute number of viral types (i.e., sequences sharing <90% L1 gene pairwise identity). Many of these novel viruses are the sole member of a novel species within a novel genus (i.e., singletons), highlighting that we have only scratched the surface of papillomavirus diversity. I will discuss how this increase in observed sequence diversity complicates papillomavirus classification. I will propose a potential solution to these issues by explicitly basing the species and genera classification on the evolutionary history of these viruses based on the core viral proteins (E1, E2, and L1) of papillomaviruses. This strategy means that it is possible that a virus identified as the closest neighbor based on the E1, E2, L1 phylogenetic tree, is not the closest neighbor based on L1 nucleotide identity. In this case, I propose that a virus would be considered a novel type if it shares less than 90% identity with its closest neighbors in the E1, E2, L1 phylogenetic tree.
Host Combats IBDV Infection at Both Protein and RNA Levels
Authors: Zhang Shujun , Zheng Shijun
Published: October 2022

Infectious bursal disease (IBD) is an acute, highly contagious, and immunosuppressive avian disease caused by infectious bursal disease virus (IBDV). In recent years, with the emergence of IBDV variants and recombinant strains, IBDV still threatens the poultry industry worldwide. It seems that the battle between host and IBDV will never end. Thus, it is urgent to develop a more comprehensive and effective strategy for the control of this disease. A better understanding of the mechanisms underlying virus–host interactions would be of help in the development of novel vaccines. Recently, much progress has been made in the understanding of the host response against IBDV infection. If the battle between host and IBDV at the protein level is considered the front line, at the RNA level, it can be taken as a hidden line. The host combats IBDV infection at both the front and hidden lines. Therefore, this review focuses on our current understanding of the host response to IBDV infection at both the protein and RNA levels.
SARS-CoV-2 from COVID-19 Patients in the Republic of Moldova: Whole-Genome Sequencing Results
Authors: Morozov Alexandr , Nirca Vadim , Victorova Anna , Poppert Sven , Frickmann Hagen , Yamada Chiaki , Kacena Melissa A. , Rata Sergiu , Movila Alexandru
Published: October 2022

Since the onset of the COVID-19 pandemic, no viral genome sequences of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been documented from the Republic of Moldova, a developing country geographically located in Eastern Europe between Romania and Ukraine. Here, we report the analysis of 96 SARS-CoV-2 sequences from Delta and Omicron variants of the SARS-CoV-2 cases in the Republic of Moldova obtained between August and November 2021 and between January and May 2022. Comparison to global viral sequences showed that among the Delta variant of the SARS-CoV-2, AY.122 (n = 25), followed by AY.4.2.3 (n = 6), AY.4 (n = 5), AY.43 (n = 3), AY.98.1 (n = 3), B.1.617.2 (n = 1), AY.125 (n = 1), AY.54 (n = 1), AY.9 (n = 1), AY.126 (n = 1), and AY.33 (n = 1) were the most frequently found lineages. Furthermore, 10 lineages of the Omicron variant, namely, BA.2 (n = 14), followed by BA.2.9 (n = 10), BA.1 (n = 5), BA.1.1 (n = 5), BA.1.18 (n = 4), BA.1.15.1 (n = 3), BA.1.17.2 (n = 2), BA.1.17 (n = 2), BA.1.15 (n = 1), and BA.2.1 (n = 1) were detected. In addition, we also identified the impact of the military crisis between Russia and Ukraine, when the COVID-19 epidemiological rules collapsed, on the distribution of Delta and Omicron variants in the Republic of Moldova. Additional studies are warranted to characterize further the impact of the war between Russia and Ukraine on the genomic epidemiology of the SARS-CoV-2 in the Republic of Moldova and Eastern Europe.
Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil
Authors: Souza Ueric José Borges de , Santos Raíssa Nunes dos , Giovanetti Marta , Alcantara Luiz Carlos Junior , Galvão Jucimária Dantas , Cardoso Franciano Dias Pereira , Brito Feliph Cássio Sobrinho , Franco Ana Cláudia , Roehe Paulo Michel , Ribeiro Bergmann Morais , Spilki Fernando Rosado , Campos Fabrício Souza
Published: October 2022

The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins’ strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016–2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service.
Synergistic Immunosuppression of Avian Leukosis Virus Subgroup J and Infectious Bursal Disease Virus Is Responsible for Enhanced Pathogenicity
Authors: Chen Weiguo , Chen Sheng , Nie Yu , Li Wenxue , Li Hongxin , Zhang Xinheng , Chen Feng , Xie Qingmei
Published: October 2022

In recent years, superinfections of avian leukosis virus subgroup J (ALV-J) and infectious bursal disease virus (IBDV) have been frequently observed in nature, which has led to the increasing virulence in infected chickens. However, the reason for the enhanced pathogenicity has remained unclear. In this study, we demonstrated an effective candidate model for studying the outcome of superinfections with ALV-J and IBDV in cells and specific-pathogen-free (SPF) chicks. Through in vitro experiments, we found that ALV-J and IBDV can establish the superinfection models and synergistically promote the expression of IL-6, IL-10, IFN-α, and IFN-γ in DF-1 and CEF cells. In vivo, the weight loss, survival rate, and histopathological observations showed that more severe pathogenicity was present in the superinfected chickens. In addition, we found that superinfections of ALV-J and IBDV synergistically increased the viral replication of the two viruses and inflammatory mediator secretions in vitro and in vivo. Moreover, by measuring the immune organ indexes and blood proportions of CD3+, CD4+, and CD8α+ cells, our results showed that the more severe instances of immunosuppression were observed in the superinfected chickens. In the present study, we concluded that the more severe immunosuppression induced by the synergistic viral replication of ALV-J and IBDV is responsible for the enhanced pathogenicity.
Tumor Suppressor p53 Inhibits Hepatitis B Virus Replication by Downregulating HBx via E6AP-Mediated Proteasomal Degradation in Human Hepatocellular Carcinoma Cell Lines
Authors: Lim Ha-Yeon , Han Jiwoo , Yoon Hyunyoung , Jang Kyung Lib
Published: October 2022

HBx, a multifunctional regulatory protein, plays an essential role in the replication and pathogenesis of the hepatitis B virus (HBV). In this study, we found that in human hepatoma cells, the tumor suppressor p53 downregulates HBx via ubiquitin-dependent proteasomal degradation. p53 transcriptional activity that results from HBV infection was not essential for this effect. This was shown by treatment with a potent p53 inhibitor, pifithrin-α. Instead, we found that p53 facilitated the binding of E6-associated protein (E6AP), which is an E3 ligase, to HBx and induced E6AP-mediated HBx ubiquitination in a ternary complex of p53, E6AP, and HBx. The ability of p53 to induce E6AP-mediated downregulation of HBx and inhibit HBV replication was demonstrated in an in vitro HBV infection system. This study may provide insights into the regulation of HBx and HBV replication, especially with respect to p53 status, which may also help in understanding HBV-associated tumorigenesis in patients.
Direct-Acting Antiviral Therapy for Hepatitis C Virus in Patients with BCLC Stage B/C Hepatocellular Carcinoma
Authors: Lee Shou-Wu , Chen Li-Shu , Yang Sheng-Shun , Huang Yi-Hsiang , Lee Teng-Yu
Published: October 2022

Background: The benefits of hepatitis C virus (HCV)eradication for hepatocellular carcinoma (HCC) patients in Barcelona Clinic Liver Cancer (BCLC) stage B/C remain uncertain. Methods: In this hospital-based cohort study, all HCV-infected patients with BCLC stage B/C HCC during the period January 2017 to March 2021 were retrospectively screened, with 97 patients who had completed direct-acting antiviral (DAA) therapy being enrolled for final analysis. Results: In total, the sustained virological response (SVR) rate was 90.7%. In logistic regression analysis, progressive disease (PD) to prior tumor treatments was significantly associated with SVR failure (odds ratio 5.59, 95% CI 1.30–24.06, p = 0.021). Furthermore, the overall survival (OS) rate was significantly higher in the SVR group than that in the non-SVR group (1-year OS: 87.5% vs. 57.1%, p = 0.001). SVR was found to be an independent factor related to OS (hazard ratio 8.42, 95% CI 2.93–24.19, p = 0.001). However, even upon achieving SVR, the OS rates in BCLC stage C or Child–Pugh stage B patients remained poor. Conclusions: In BCLC stage B/C HCC, DAA could achieve a high SVR rate except in those patients with PD to prior HCC treatments. SVR was related to improvements in OS; therefore, DAA therapy should be encouraged for patients diagnosed without a short life expectancy.
Development of a Next-Generation Vaccine Platform for Porcine Epidemic Diarrhea Virus Using a Reverse Genetics System
Authors: Jang Guehwan , Lee Duri , Lee Changhee
Published: October 2022

For the past three decades, the porcine epidemic diarrhea virus (PEDV) has remained an enormous threat to the South Korean swine industry. The scarcity of an effective method for manipulating viral genomes has impeded research progress in PEDV biology and vaccinology. Here, we report the development of reverse genetics systems using two novel infectious full-length cDNA clones of a Korean highly pathogenic-G2b strain, KNU-141112, and its live attenuated vaccine strain, S DEL5/ORF3, in a bacterial artificial chromosome (BAC) under the control of a eukaryotic promoter. Direct transfection of cells with each recombinant BAC clone induced cytopathic effects and produced infectious progeny. The reconstituted viruses, icKNU-141112 and icS DEL5/ORF3, harboring genetic markers, displayed phenotypic and genotypic properties identical to their respective parental viruses. Using the DNA-launched KNU-141112 infectious cDNA clone as a backbone, two types of recombinant viruses were generated. First, we edited the open reading frame 3 (ORF3) gene, as cell-adapted strains lose full-length ORF3, and replaced this region with an enhanced green fluorescent protein (EGFP) gene to generate icPEDV-EGFP. This mutant virus presented parental virus-like growth kinetics and stably retained robust EGFP expression, indicating that ORF3 is dispensable for PEDV replication in cell culture and is a tolerant location for exogeneous gene acceptance. However, the plaque size and syncytia phenotypes of ORF3-null icPEDV-EGFP were larger than those of icKNU-141112 but similar to ORF3-null icS DEL5/ORF3, suggesting a potential role of ORF3 in PEDV cytopathology. Second, we substituted the spike (S) gene with a heterologous S protein, designated S51, from a variant of interest (VOI), which was the most genetically and phylogenetically distant from KNU-141112. The infectious recombinant VOI, named icPEDV-S51, could be recovered, and the rescued virus showed indistinguishable growth characteristics compared to icKNU-141112. Virus cross-neutralization and structural analyses revealed antigenic differences in S between icKNU-141112 and icPEDV-S51, suggesting that genetic and conformational changes mapped within the neutralizing epitopes of S51 could impair the neutralization capacity and cause considerable immune evasion. Collectively, while the established molecular clones afford convenient, versatile platforms for PEDV genome manipulation, allowing for corroborating the molecular basis of viral replication and pathogenesis, they also provide key infrastructural frameworks for developing new vaccines and coronaviral vectors.
Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody
Authors: Qi Shuai , Fu Wangjun , Fan Jinyan , Zhang Li , Zheng Binyang , Wang Kang , Wang Xiangxi , Zhu Ling , Li Xinjian , Zhang Yuxia
Published: October 2022

Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to comprehensively understand the specificities and the immunological characteristic of this serotype. The solved cryo-EM structures of the F-, A-, and E-particles of E3 bound with 6D10 revealed the structural features of the virus–antibody interface. Importantly, the structures of E-particles bound with 6D10 revealed for the first time the nature of the C-terminus of VP1 for HEV-Bs at the structural level. The highly immunogenic nature of this region in the E-particles provides new strategies for vaccine development for HEV-Bs.
An Update on Detection Technologies for SARS-CoV-2 Variants of Concern
Authors: Jiang Wenjie , Ji Wangquan , Zhang Yu , Xie Yaqi , Chen Shuaiyin , Jin Yuefei , Duan Guangcai
Published: October 2022

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is responsible for the global epidemic of Coronavirus Disease 2019 (COVID-19), with a significant impact on the global economy and human safety. Reverse transcription-quantitative polymerase chain reaction (RT-PCR) is the gold standard for detecting SARS-CoV-2, but because the virus’s genome is prone to mutations, the effectiveness of vaccines and the sensitivity of detection methods are declining. Variants of concern (VOCs) include Alpha, Beta, Gamma, Delta, and Omicron, which are able to evade recognition by host immune mechanisms leading to increased transmissibility, morbidity, and mortality of COVID-19. A range of research has been reported on detection techniques for VOCs, which is beneficial to prevent the rapid spread of the epidemic, improve the effectiveness of public health and social measures, and reduce the harm to human health and safety. However, a meaningful translation of this that reduces the burden of disease, and delivers a clear and cohesive message to guide daily clinical practice, remains preliminary. Herein, we summarize the capabilities of various nucleic acid and protein-based detection methods developed for VOCs in identifying and differentiating current VOCs and compare the advantages and disadvantages of each method, providing a basis for the rapid detection of VOCs strains and their future variants and the adoption of corresponding preventive and control measures.
The Molecular Characterization of a New Prunus-Infecting Cheravirus and Complete Genome Sequence of Stocky Prune Virus
Authors: Khalili Maryam , Candresse Thierry , Brans Yoann , Faure Chantal , Audergon Jean-Marc , Decroocq Véronique , Roch Guillaume , Marais Armelle
Published: October 2022

As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests that the new virus should be considered a new species for which the name alpine wild prunus virus (AWPV) is proposed. In parallel, the complete genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed that AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses.
Blood Center Testing Allows the Detection and Rapid Treatment of Acute and Recent HIV Infection
Authors: van den Berg Karin , Vermeulen Marion , Bakkour Sonia , Stone Mars , Jacobs Genevieve , Nyoni Cynthia , Barker Coreen , McClure Christopher , Creel Darryl , Grebe Eduard , Roubinian Nareg , Jentsch Ute , Custer Brian , Busch Michael P. , Murphy Edward L. ,   on behalf of the Recipient Epidemiology and Donor Evaluation Study (REDS)-III South Africa International Program
Published: October 2022

Blood donations in South Africa are tested for HIV RNA using individual donation NAT (ID-NAT), allowing detection and rapid antiretroviral therapy (ART) of acute HIV infections. We enrolled a cohort of acute and recent HIV-infected blood donation candidates in South Africa in 2015–2018, measured HIV antibody, ID-NAT, and recency of infection <195 days (Sedia LAg) at enrollment and initiated early ART. A small cohort of HIV elite controllers was followed without treatment. HIV reservoir measurements included ultrasensitive plasma RNA, cell-associated HIV RNA, and total DNA. Enrollment of 18 Fiebig I–III and 45 Fiebig IV–VI HIV clade C subjects occurred a median of 18 days after index blood donation. ART was administered successfully and compliance with follow-up visits was excellent. There were only minimal differences in HIV reservoir between ART initiation in Fiebig stages I–III vs. IV–VI, but ART noncompliance increased HIV reservoir. In 11 untreated HIV elite controllers, HIV reservoir levels were similar to or higher than those seen in our early treated cohort. National blood services can identify acute HIV cohorts for subsequent HIV cure research studies. Among HIV clade C-infected donors, HIV reservoir differed little by Fiebig stage at treatment initiation, but was smaller than in chronically treated HIV and those with ART noncompliance.