bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of Measurement Accuracy of Bridge Deformation Using UAV-Based Oblique Photography Technique
Authors: He Shaohua , Guo Xiaochun , He Jianyan , Guo Bo , Zheng Cheng
Published: September 2022

This paper investigates the measurement accuracy of unmanned aerial vehicle-based oblique photography (UAVOP) in bridge deformation identifications. A simply supported concrete beam model was selected and measured using the UAVOP technique. The influences of several parameters, such as overall flight altitude (h), local shooting distance (d), partial image overlap (λ), and arrangement of control points, on the quality of the reconstructed three-dimensional (3D) beam model, were presented and discussed. Experimental results indicated that the quality of the reconstructed 3D model was significantly improved by the fusion overall-partial flight routes (FR), of which the reconstructed model quality was 46.7% higher than those with the single flight route (SR). Despite the minimal impact of overall flight altitude, the reconstructed model quality prominently varied with the local shooting distance, partial image overlap, and control points arrangement. As the d decreased from 12 m to 8 m, the model quality was improved by 48.2%, and an improvement of 42.5% was also achieved by increasing the λ from 70% to 80%. The reconstructed model quality of UAVOP with the global-plane control points was 78.4% and 38.4%, respectively, higher than those with the linear and regional control points. Furthermore, an optimized scheme of UAVOP with control points in global-plane arrangement and FR (h = 50 m, d = 8 m, and λ = 80%) was recommended. A comparison between the results measured by the UAVOP and the total station showed maximum identification errors of 1.3 mm. The study’s outcomes are expected to serve as potential references for future applications of UAVOP in bridge measurements.
The Influence of Plastic Barriers on Aerosol Infection Risk during Airport Security Checks
Authors: Zhu Shengwei , Lin Tong , Spengler John D. , Cedeño Laurent Jose Guillermo , Srebric Jelena
Published: September 2022

Plastic barriers physically separate queuing passengers in airport security check areas as a measure against aerosol transmission. However, this may create “canyons” that interfere with the existing ventilation design: potentially inhibiting airflow, concentrating exhaled viruses, and exacerbating aerosol transmission risk. Accordingly, this study investigated the transmission implications of installing plastic barriers in a security check area with computational fluid dynamics (CFD). Two air distribution schemes were modeled: one with linear air supply diffusers aligned vertically to (Case 1) and another with diffusers parallel with (Case 2) the orientation of partitions. The drift-flux model was used to calculate the spread of viral bioaerosols with 5 µm in diameter; then the Wells–Riley equation was applied to assess aerosol transmission risk for SARS-CoV-2. According to simulation results, in Case 1, installing plastic barriers resulted in relatively small changes in volume with a high infection risk of 1% or greater in the breathing zone within the first 25 min. However, in Case 2, using plastic barriers resulted in the continuous increase in this volume within the first 25 min while this volume was near zero if without plastic barriers. In conclusion, installing plastic barriers needs careful consideration because they do not reduce the risk of airborne SARS-CoV-2 transmission and might even exacerbate it without localized ventilation and air cleaning.
Impacts of Rainstorm Characteristics on Runoff Quantity and Quality Control Performance Considering Integrated Green Infrastructures
Authors: Zhang Dongqing , Mei Chao , Ding Xiangyi , Liu Jiahong , Fu Xiaoran , Wang Jia , Wang Dong
Published: September 2022

Green infrastructure (GI) has been implemented globally to mitigate the negative effects of urbanization. GI also regulates the urban runoff process and reduces non-point source pollution by intercepting initial runoff pollution and stormwater storage. In this paper, the impacts on GI were quantified and analyzed, considering eight designed storms with a 24 h duration and eight others with a 2 h duration with the combination of two characteristics (return period and peak time). The runoff process and reduction effect of pollutants were simulated for GI combinations (green roofs, vegetative swale, bio-retention units, and permeable pavement) using the Storm Water Management Model, taking the Dongshan campus of Shanxi University as an example case study. The results show that the GI combination can reduce runoff, suspended solids (SS), and chemical oxygen demand (COD). For short- and long-duration rainstorms, the average reduction rates of runoff, SS, and COD were 39.7%, 38.8%, and 39.6%, and 36.5%, 31.7%, and 32%, respectively, indicating its better effectiveness for short-duration storms. The GI’s effect was more sensitive during the short-duration storms owing to the greater absolute value of the 2 h elastic coefficients versus that of the 24 h, and the best reduction effect was observed with a rainfall peak coefficient of 0.1. These results provide a scientific reference for GI planning and implementation under a changing climate in the future.
Mineral Texture Identification Using Local Binary Patterns Equipped with a Classification and Recognition Updating System (CARUS)
Authors: Aligholi Saeed , Khajavi Reza , Khandelwal Manoj , Armaghani Danial Jahed
Published: September 2022

In this paper, a rotation-invariant local binary pattern operator equipped with a local contrast measure (riLBPc) is employed to characterize the type of mineral twinning by inspecting the texture properties of crystals. The proposed method uses photomicrographs of minerals and produces LBP histograms, which might be compared with those included in a predefined database using the Kullback–Leibler divergence-based metric. The paper proposes a new LBP-based scheme for concurrent classification and recognition tasks, followed by a novel online updating routine to enhance the locally developed mineral LBP database. The discriminatory power of the proposed Classification and Recognition Updating System (CARUS) for texture identification scheme is verified for plagioclase, orthoclase, microcline, and quartz minerals with sensitivity (TPR) near 99.9%, 87%, 99.9%, and 96%, and accuracy (ACC) equal to about 99%, 97%, 99%, and 99%, respectively. According to the results, the introduced CARUS system is a promising approach that can be applied in a variety of different fields dealing with classification and feature recognition tasks.
Evaluating and Prioritizing the Enablers of Supply Chain Performance Management System (SCPMS) for Sustainability
Authors: Qureshi Mohamed Rafik Noor Mohamed
Published: September 2022

A business organization needs a supply chain performance management system (SCPMS) to build an effective and efficient supply chain (SC) that will provide much-needed sustainability. The performance evaluation of supply chain management (SCM) is difficult and needs consideration of several important enablers. In such situations, the development of an SCPMS can facilitate understanding and integration among the SC partners. The SCPMS is influenced by many enablers that play a positive role; hence, the study of these enablers becomes significant. Therefore, the purpose of this study was to identify and rank the key SCPMS enablers. The identified SCPMS enablers were modeled using interpretive structural modeling (ISM) and ranked through an interpretative ranking process (IRP). The SCPMS enablers were further categorized using MICMAC. The results show that “SCPMS awareness”, “top management commitment”, and “financial commitment towards SCPMS” must be controlled for sustainability as they are independent enablers. “Benchmarking”, “appropriate performance matrix”, and “employee commitment” were the three top enablers.
Mechanical and Durability Properties of Self-Compacted Concrete Incorporating Waste Crumb Rubber as Sand Replacement: A Review
Authors: Zrar Yarivan J. , Younis Khaleel H.
Published: September 2022

The lack of disposal facilities for waste tires from various vehicles is a major environmental and economic problem. Crumb rubber (CR) generated from waste tires can be used to partially replace fine natural aggregates in self-compacted concrete (SCC), lowering sand usage and protecting raw material resources. The main objective of this study is to summarize the influence of CR as a partial replacement for sand on the behavior of SCC. For this aim, 42 papers were selected out of 89 that were relevant to the objective of this study. The mechanical properties, i.e., compressive strength, flexural strength, splitting tensile strength, modulus of elasticity, and bond strength, as well as the ultrasonic pulse velocity (UPV), were all reduced by the insertion of CR into SCC mixtures. With the addition of CR, fracture energy decreases, but the ductility of concrete in terms of characteristic length can be enhanced. Meanwhile, replacing sand with CR can also reduce the durability performance of SCC, such as sorptivity, free-drying shrinkage, rapid chloride permeability, and depth of chloride penetration, except for the electrical resistivity, depth of carbonation, and impact resistance, which exhibit a positive tendency. Based on the results of the reviewed articles, predicted reductions in the strength of the SCC incorporating CR were also recommended. Moreover, the results of the reviewed studies were employed to develop empirical models that demonstrate the relations between various mechanical properties.
Assessing ASEAN’s Liberalized Electricity Markets: The Case of Singapore and the Philippines
Authors: Ali Hassan , Phoumin Han , Suryadi Beni , Farooque Aitazaz A. , Yaqub Raziq
Published: September 2022

The efforts towards the liberalization of electricity markets have sped up recently in some countries within the Association of Southeast Asian Nations (ASEAN) region. This step of opening up the electricity markets is aimed at establishing competitive and efficient electricity markets that not only reduce electricity prices, but also support a sustainable future by reducing carbon dioxide (CO2) emissions from electricity generation and promoting the wider adoption of renewable energy (RE)-based electricity generation. This paper assesses the effects of the electricity market liberalization process in Singapore and the Philippines on these expected outcomes during the period 2015–2020. The regression analysis results suggest that in the specified period, the liberalization of the electricity market in Singapore has delivered both household and industry electricity price reductions and improvement in the RE share. However, there is no significant effect of the electricity market liberalization process on the electricity generated CO2 emissions. For the same period, the results imply that with the electricity market liberalization process in the Philippines, the electricity prices for household consumers and electricity-generated CO2 emissions have increased. Additionally, the liberalization process has no significant impact on both the RE share and industry electricity prices in the Philippines. To overcome the obstacles and strike a balance between the expected outcomes, policy recommendations are given for ASEAN economies following the pathway of liberalized electricity markets.
Can Carbon Neutrality Commitment Contribute to the Sustainable Development of China’s New Energy Companies?
Authors: Deng Jing , Zhang Yun , Xing Xiaoyun , Liu Cheng
Published: September 2022

Developing new energy is one of the most important measures to implement global carbon neutrality. Under the constraints of carbon emission reduction, the question of how to achieve the sustainable development of new energy enterprises has become an important issue among managers and investors. This study selects Chinese listed companies in the new energy industry as the research sample, employs the DID method and uses panel data to explore the role of carbon neutrality commitment in the sustainable growth of new energy companies. The results show that the carbon neutrality commitment has greatly improved the sustainable development of Chinese new energy companies, with the internal profitability and external investor sentiment of the enterprises being important mediating variables. Moreover, the effect of the carbon neutrality commitment on the sustainable growth of non-state-owned new energy firms is much more significant compared with that of state-owned enterprises, and the effect is more robust in the east than in the central and western regions. Based on the conclusions, this study provides practical implications for managers, investors and policymakers in order to promote the sustainable growth of new energy firms.
Automatic Segmentation and Classification System for Foliar Diseases in Sunflower
Authors: Dawod Rodica Gabriela , Dobre Ciprian
Published: September 2022

Obtaining a high accuracy in the classification of plant diseases using digital methods is limited by the diversity of conditions in nature. Previous studies have shown that classification of diseases made with images of lesions caused by diseases is more accurate than a classification made with unprocessed images. This article presents the results obtained when classifying foliar diseases in sunflower using a system composed of a model that automatically segments the leaf lesions, followed by a classification system. The segmentation of the lesions was performed using both Faster R-CNN and Mask R-CNN. For the classification of diseases based on lesions, the residual neural networks ResNet50 and ResNet152 were used. The results show that automatic segmentation of the lesions can be successfully achieved in the case of diseases such as Alternaria and rust, in which the lesions are well-outlined. In more than 90% of the images, at least one affected area has been segmented. Segmentation is more difficult to achieve in the cases of diseases such as powdery mildew, in which the entire leaf acquires a whitish color. Diseased areas could not be segmented in 30% of the images. This study concludes that the use of a system composed of a network that segments lesions, followed by a network that classifies diseases, allows us to both more accurately classify diseases and identify those images for which a precise classification cannot be made.
Urban Expansion and Its Implication to Build Urban Resilience in Regio-Metropolitan Cities of the Amahara Region, Ethiopia
Authors: Gashu Kassahun , Alene Endalew Terefe
Published: September 2022

There could be many empirical contexts which could be applied in urban resilience. The general objective of this research is to assess urban expansion and its implication on urban resilience in regio-metropolitan cities in the Amhara Region (Gondar and Bahir Dar). It used mixed research approaches and cross-sectional design. Data were collected from primary and secondary sources. Primary data were collected from a survey questionnaire, key informant interview and FGDs while secondary data were gathered from both published and unpublished sources. A multi-stage sampling technique was used to determine sample size, and a proportional sampling method was used. Quantitative data were analyzed using descriptive statistics (mean, percentage, SD), while qualitative data were analyzed using thematic analysis. The results indicate that major factors that influence building urban resilience are lacking proper urban planning, basic infrastructure and good governance in both cities, and both cities are extremely far behind in implementing urban resilience principles. Hence, the study improves the community participation in development policy formulation and implementation for urban resilience.
Understanding Sources and Composition of Black Carbon and PM2.5 in Urban Environments in East India
Authors: Ambade Balram , Sankar Tapan Kumar , Sahu Lokesh K. , Dumka Umesh Chandra
Published: September 2022

Black carbon (BC) and PM2.5 chemical characterizations are crucial for insight into their impact on the health of the exposed population. PM2.5 sampling was carried out over selected residential sites of Jamshedpur (JSR) and Kharagpur (KGP), east India, during the winter season. Seven selected elements (SO42−, Cl−, Na+, NO3−, K+, Ca2+, and Mg2+) were analyzed using ion chromatography (IC). Black carbon (BC) sampling was also done at two different sites in JSR and KGP to understand its correlation. The PM2.5 ionic species mass concentration in JSR was in the order of SO42− > Cl− > Na+ > NO3− > K+ > Ca2+ > Mg2+, whereas in KGP, it was SO42− > NO3− > Cl− > Na+ > K+ > Ca2+ > Mg2+. The back-trajectory analysis showed that most of the air masses during the study period originated from the Indo Gangetic Plain (IGP). The Pearson relations of BC-PM2.5 indicate a better positive correlation (r = 0.66) at KGP compared to JSR (r = 0.42). As shown in the diagnostic ratio analysis, fossil fuel combustion and wood burning account for 51.51% and 36.36% of the total energy consumption in JSR city, respectively. In KGP city, the apportionment of origin sources were fossil fuel and wood burning at 43.75% and 34.37%, respectively. This study provides the first inventory of atmospheric particulate-bound chemical concentrations and BC profiles in middle-east India and informs policymakers and scientists for further studies.
An Adenoviral Vector as a Versatile Tool for Delivery and Expression of miRNAs
Authors: Scholz Jonas , Weil Patrick Philipp , Pembaur Daniel , Koukou Georgia , Aydin Malik , Hauert Dorota , Postberg Jan , Kreppel Florian , Hagedorn Claudia
Published: September 2022

Only two decades after discovering miRNAs, our understanding of the functional effects of deregulated miRNAs in the development of diseases, particularly cancer, has been rapidly evolving. These observations and functional studies provide the basis for developing miRNA-based diagnostic markers or new therapeutic strategies. Adenoviral (Ad) vectors belong to the most frequently used vector types in gene therapy and are suitable for strong short-term transgene expression in a variety of cells. Here, we report the set-up and functionality of an Ad-based miRNA vector platform that can be employed to deliver and express a high level of miRNAs efficiently. This vector platform allows fast and efficient vector production to high titers and the expression of pri-miRNA precursors under the control of a polymerase II promoter. In contrast to non-viral miRNA delivery systems, this Ad-based miRNA vector platform allows accurate dosing of the delivered miRNAs. Using a two-vector model, we showed that Ad-driven miRNA expression was sufficient in down-regulating the expression of an overexpressed and highly stable protein. Additional data corroborated the downregulation of multiple endogenous target RNAs using the system presented here. Additionally, we report some unanticipated synergistic effects on the transduction efficiencies in vitro when cells were consecutively transduced with two different Ad-vectors. This effect might be taken into consideration for protocols using two or more different Ad vectors simultaneously.
A How to Guide: Clinical Population Test Development and Authorization of MALDI-ToF Mass Spectrometry-Based Screening Tests for Viral Infections
Authors: Iles Ray , Iles Jason , Zmuidinaite Raminta , Roberts Michael
Published: September 2022

Applying MALDI-ToF mass spectrometry as a clinical diagnostic test for viruses is different from that of bacteria, fungi and other micro-organisms. This is because the systems biology of viral infections, the size and chemical nature of specific viral proteins and the mass spectrometry biophysics of how they are quantitated are fundamentally different. The analytical challenges to overcome when developing a clinical MALDI-ToF mass spectrometry tests for a virus, particularly human pathogenic enveloped viruses, are sample enrichment, virus envelope disruption, optimal matrix formulation, optimal MALDI ToF MS performance and optimal spectral data processing/bioinformatics. Primarily, the instrument operating settings have to be optimized to match the nature of the viral specific proteins, which are not compatible with setting established when testing for bacterial and many other micro-organisms. The capacity to be a viral infection clinical diagnostic instrument often stretches current mass spectrometers to their operational design limits. Finally, all the associated procedures, from sample collection to data analytics, for the technique have to meet the legal and operational requirement for often high-throughput clinical testing. Given the newness of the technology, clinical MALDI ToF mass spectrometry does not fit in with standard criteria applied by regulatory authorities whereby numeric outputs are compared directly to similar technology tests that have already been authorized for use. Thus, CLIA laboratory developed test (LDT) criteria have to be applied. This article details our experience of developing a SAR-CoV-2 MALDI-ToF MS test suitable for asymptomatic carrier infection population screening.
Inhibition of Cell-Free Translation and Replication of Tobacco Mosaic Virus RNA by Exogenously Added 5′-Proximal Fragments of the Genomic RNA
Authors: Yoshida Tetsuya , Ishikawa Masayuki , Ishibashi Kazuhiro
Published: September 2022

Replication proteins of tobacco mosaic virus (TMV), a positive-sense RNA virus, co-translationally bind to a 5′-proximal ~70-nucleotide (nt) region of the genomic RNA, referred to as the nuclease-resistant (NR) region for replication template selection. Therefore, disruption of the interaction between the viral replication proteins and viral genomic RNA is expected to inhibit the replication of TMV. In this study, we demonstrate that the addition of small RNA fragments (18–33 nts in length) derived from different regions within the NR region inhibit the binding of TMV replication proteins to viral RNA and TMV RNA replication in a cell-free system. Intriguingly, some of the small RNA fragments also inhibited the translation of mRNA in a sequence-nonspecific manner. These results highlight the pleiotropic roles of the 5′-proximal region of the TMV genome.
Lethal Disease in Dogs Naturally Infected with Severe Fever with Thrombocytopenia Syndrome Virus
Authors: Ishijima Keita , Tatemoto Kango , Park Eunsil , Kimura Masanobu , Fujita Osamu , Taira Masakatsu , Kuroda Yudai , Mendoza Milagros Virhuez , Inoue Yusuke , Harada Michiko , Matsuu Aya , Shimoda Hiroshi , Kuwata Ryusei , Morikawa Shigeru , Maeda Ken
Published: September 2022

Severe fever with the thrombocytopenia syndrome virus (SFTSV) causes fatal disease in humans, cats, and cheetahs. In this study, the information on seven dogs with SFTS was summarized. All dogs showed anorexia, high fever, leukopenia, and thrombocytopenia, two dogs showed vomiting and loose stool, and five dogs had tick parasites. All dogs also had a history of outdoor activity. The SFTSV gene was detected in all dogs. Remarkably, three dogs (43%) died. SFTSV was isolated from six dogs and the complete genomes were determined. A significant increase in anti-SFTSV-IgG antibodies was observed in two dogs after recovery, and anti-SFTSV-IgM antibodies were detected in four dogs in the acute phase. Using an ELISA cut-off value of 0.410 to discriminate between SFTSV-negative and positive dogs, the detection of anti-SFTSV-IgM antibodies was useful for the diagnosis of dogs with acute-phase SFTS. Four out of the ninety-eight SFTSV-negative dogs possessed high anti-SFTSV IgG antibody titers, indicating that some dogs can recover from SFTSV infection. In conclusion, SFTSV is lethal in some dogs, but many dogs recover from SFTSV infection.
Hazara Orthonairovirus Nucleoprotein Antagonizes Type I Interferon Production by Inhibition of RIG-I Ubiquitination
Authors: Ohta Keisuke , Saka Naoki , Nishio Machiko
Published: September 2022

Viruses have evolved various strategies to evade the host innate immune system. The relationship between nairoviruses and the interferon (IFN) system is poorly understood. We investigated whether and how nairoviruses antagonize host innate immunity using Hazara orthonairovirus (HAZV) as a surrogate model for Crimean-Congo hemorrhagic fever virus. HAZV nucleoprotein (N) was found to interact with the tripartite motif-containing protein 25 (TRIM25). The N-terminal region of N protein and the C-terminal region of TRIM25 are important for their interaction. Overexpression of N protein results in weakened interaction of TRIM25 with retinoic acid-inducible gene I (RIG-I). Furthermore, K63-linked polyubiquitination of RIG-I is inhibited in the presence of N protein. Our data collectively suggest that HAZV N protein interferes with the binding of TRIM25 to RIG-I and subsequent K63-linked polyubiquitination of RIG-I, which leads to inhibition of type I IFN production.
Correction: Lesbon et al. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses 2021, 13, 2474
Authors: Lesbon Jéssika Cristina Chagas , Poleti Mirele Daiana , de Mattos Oliveira Elisângela Chicaroni , Patané José Salvatore Leister , Clemente Luan Gaspar , Viala Vincent Louis , Ribeiro Gabriela , Giovanetti Marta , de Alcantara Luiz Carlos Junior , Teixeira Olivia , Nonato Maria Cristina , de Lima Loyze Paola Oliveira , Martins Antonio Jorge , dos Santos Barros Claudia Renata , Marqueze Elaine Cristina , de Souza Todão Bernardino Jardelina , Moretti Debora Botequio , Brassaloti Ricardo Augusto , de Lello Rocha Campos Cassano Raquel , Mariani Pilar Drummond Sampaio Correa , Slavov Svetoslav Nanev , dos Santos Rafael Bezerra , Rodrigues Evandra Strazza , Santos Elaine Vieira , Borges Josiane Serrano , de La Roque Debora Glenda Lima , Kitajima Joao Paulo , Santos Bibiana , Assato Patricia Akemi , da Silva da Costa Felipe Allan , Banho Cecilia Artico , Sacchetto Livia , Moraes Marilia Mazzi , Palmieri Melissa , da Silva Fabiana Erica Vilanova , Grotto Rejane Maria Tommasini , Souza-Neto Jayme A. , Nogueira Mauricio Lacerda , Coutinho Luiz Lehman , Calado Rodrigo Tocantins , Neto Raul Machado , Covas Dimas Tadeu , Kashima Simone , Elias Maria Carolina , Sampaio Sandra Coccuzzo , Fukumasu Heidge
Published: September 2022

The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in Viruses entitled “Nucleocapsid (N) gene mutations of SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results” [...]
HIV-1 Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs) in Israel, 2010–2018
Authors: Wagner Tali , Zuckerman Neta S. , Wax Marina , Shirazi Rachel , Gozlan Yael , Girshengorn Shirley , Marom Rotem , Mendelson Ella , Turner Dan , Mor Orna
Published: September 2022

Monitoring HIV-1 circulating recombinant forms (CRFs) and unique recombinant forms (URFs) is important for disease surveillance. Recombination may affect prevention efforts and interfere with the diagnosis and treatment of HIV-1 infection. Here, we characterized the epidemiology of HIV-1 CRFs and URFs in Israel. Partial pol sequences from treatment naïve patients diagnosed in 2010–2018 were assessed using the recombinant identification program (RIP), the recombinant detection program (RDP5), and using the maximum-likelihood phylogenetic method, using 410 reference sequences obtained from the Los Alamos database. CRFs and URFs were identified in 11% (213/1940) of all sequenced cases. The median age at diagnosis was 38 (30–47) years, 61% originated from Israel, and 82% were male. The most common were CRF02_AG (30.5%), CRF01_AE (16.9%), and the more complex forms CRF01_AE/CRF02_AG/A3 (10.8%) and B/F1 (7%). A significant increase in their overall proportion was observed in recent years (8.1% in 2010–2012, 20.3% in 2016–2018, p < 0.001). This increase was most prominent in individuals carrying CRF02_AG (2.5% in 2010–2015, 9.8% in 2016–2018, p < 0.001). Men who have sex with men (MSM) was the most common risk group; however, those infected with the secondary recombinant CRF02_AG/A6 were mainly injecting drug users (IDUs). The most common resistance mutations were K103N (5/213, 2.3%) and E138A (18/213, 8.5%) in the reverse transcriptase. Only E138A was more frequent in the recombinants compared with the classic subtypes and was significantly associated with a specific secondary CRF, CRF02_AG/A4. We concluded that CRFs and URFs were mainly detected in Israeli-born MSM and that an increase in the overall proportion of such HIV-1 sequences could be observed in more recent years.
Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity
Authors: Barzak Fareeda M. , Ryan Timothy M. , Mohammadzadeh Nazanin , Harjes Stefan , Kvach Maksim V. , Kurup Harikrishnan M. , Krause Kurt L. , Chelico Linda , Filichev Vyacheslav V. , Harjes Elena , Jameson Geoffrey B.
Published: September 2022

APOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although X-ray single-crystal structures of individual catalytic domains of APOBEC3G with ssDNA as well as full-length APOBEC3G have been solved recently, there is little structural information available about ssDNA interaction with the full-length APOBEC3G or any other two-domain APOBEC3. Here, we investigated the solution-state structures of full-length APOBEC3G with and without a 40-mer modified ssDNA by small-angle X-ray scattering (SAXS), using size-exclusion chromatography (SEC) immediately prior to irradiation to effect partial separation of multi-component mixtures. To prevent cytosine deamination, the target 2′-deoxycytidine embedded in 40-mer ssDNA was replaced by 2′-deoxyzebularine, which is known to inhibit APOBEC3A, APOBEC3B and APOBEC3G when incorporated into short ssDNA oligomers. Full-length APOBEC3G without ssDNA comprised multiple multimeric species, of which tetramer was the most scattering species. The structure of the tetramer was elucidated. Dimeric interfaces significantly occlude the DNA-binding interface, whereas the tetrameric interface does not. This explains why dimers completely disappeared, and monomeric protein species became dominant, when ssDNA was added. Data analysis of the monomeric species revealed a full-length APOBEC3G–ssDNA complex that gives insight into the observed “jumping” behavior revealed in studies of enzyme processivity. This solution-state SAXS study provides the first structural model of ssDNA binding both domains of APOBEC3G and provides data to guide further structural and enzymatic work on APOBEC3–ssDNA complexes.
HTLV-1/2 Infection in Blood Donors from a Non-Endemic Area (Catalonia, Spain) between 2008 and 2017: A 10-Year Experience
Authors: Piron Maria , Salvador Fernando , Caballero Estrella , Sánchez-Montalvá Adrián , Bes Marta , Casamitjana Natàlia , Puig Lluís , Molina Israel , Sauleda Silvia
Published: September 2022

Human T-cell lymphotropic virus type 1 and 2 (HTLV-1/2) screening is not mandatory in Spanish blood banks. In Catalonia, selective screening was introduced in 2008, followed by universal screening in 2011. We present herein a 10-year experience of HTLV testing in blood donors. HTLV-1/2 selective screening was performed using Ortho-Clinical Diagnostics HTLV-I/HTLV-II Ab-Capture ELISA between February 2008 and May 2009, then Abbott Prism HTLV-I/ HTLV-II assay until December 2010. Abbott Architect rHTLV-I/II assay was then used for HTLV-1/2 universal screening in pooled samples. INNO-LIA HTLV I/II Score (Fujirebio) and in-house HTLV-1/2 proviral DNA real-time PCR were used in reactive samples. Follow-up was offered to confirm HTLV-1/2 donors in Vall d’Hebron Hospital. Between 2008 and 2017, 51 blood donors were confirmed HTLV positive (46 HTLV-1, 4 HTLV-2 and 1 HTLV) out of 2,114,891 blood donations (1 in 41,468). Sixty-nine percent were female, median age was 40 years and most were born in Latin America (69%), followed by Europe (25%), Africa (4%) and Asia (2%). Screening of relatives and partners identified 12 additional HTLV-1 cases. Lookback studies did not show any HTLV-1/2 transmission. HTLV infections found in blood donors mirror epidemiological changes in the population of Spain. Consequently, HTLV should be considered a potential risk for recipients and calls for the design of optimal strategies to ensure transfusion safety.
Association of the Transmembrane Serine Protease-2 (TMPRSS2) Polymorphisms with COVID-19
Authors: Posadas-Sánchez Rosalinda , Fragoso José Manuel , Sánchez-Muñoz Fausto , Rojas-Velasco Gustavo , Ramírez-Bello Julian , López-Reyes Alberto , Martínez-Gómez Laura E. , Sierra-Fernández Carlos , Rodríguez-Reyna Tatiana , Regino-Zamarripa Nora Elemi , Ramírez-Martínez Gustavo , Zuñiga-Ramos Joaquín , Vargas-Alarcón Gilberto
Published: September 2022

SARS-CoV-2 uses the ACE2 receptor and the cellular protease TMPRSS2 for entry into target cells. The present study aimed to establish if the TMPRSS2 polymorphisms are associated with COVID-19 disease. The study included 609 patients with COVID-19 confirmed by RT-PCR test and 291 individuals negative for the SARS-CoV-2 infection confirmed by RT-PCR test and without antibodies anti-SARS-CoV-2. Four TMPRSS2 polymorphisms (rs12329760, rs2298659, rs456298, and rs462574) were determined using the 5′exonuclease TaqMan assays. Under different inheritance models, the rs2298659 (pcodominant2 = 0.018, precessive = 0.006, padditive = 0.019), rs456298 (pcodominant1 = 0.014, pcodominant2 = 0.004; pdominant = 0.009, precessive = 0.004, padditive = 0.0009), and rs462574 (pcodominant1 = 0.017, pcodominant2 = 0.004, pdominant = 0.041, precessive = 0.002, padditive = 0.003) polymorphisms were associated with high risk of developing COVID-19. Two risks (ATGC and GAAC) and two protectives (GAGC and GAGT) haplotypes were detected. High levels of lactic acid dehydrogenase (LDH) were observed in patients with the rs462574AA and rs456298TT genotypes (p = 0.005 and p = 0.020, respectively), whereas, high heart rate was present in patients with the rs462574AA genotype (p = 0.028). Our data suggest that the rs2298659, rs456298, and rs462574 polymorphisms independently and as haplotypes are associated with the risk of COVID-19. The rs456298 and rs462574 genotypes are related to high levels of LDH and heart rate.
Apprehending the NAD+–ADPr-Dependent Systems in the Virus World
Authors: Iyer Lakshminarayan M. , Burroughs A. Maxwell , Anantharaman Vivek , Aravind L.
Published: September 2022

NAD+ and ADP-ribose (ADPr)-containing molecules are at the interface of virus–host conflicts across life encompassing RNA processing, restriction, lysogeny/dormancy and functional hijacking. We objectively defined the central components of the NAD+–ADPr networks involved in these conflicts and systematically surveyed 21,191 completely sequenced viral proteomes representative of all publicly available branches of the viral world to reconstruct a comprehensive picture of the viral NAD+–ADPr systems. These systems have been widely and repeatedly exploited by positive-strand RNA and DNA viruses, especially those with larger genomes and more intricate life-history strategies. We present evidence that ADP-ribosyltransferases (ARTs), ADPr-targeting Macro, NADAR and Nudix proteins are frequently packaged into virions, particularly in phages with contractile tails (Myoviruses), and deployed during infection to modify host macromolecules and counter NAD+-derived signals involved in viral restriction. Genes encoding NAD+–ADPr-utilizing domains were repeatedly exchanged between distantly related viruses, hosts and endo-parasites/symbionts, suggesting selection for them across the virus world. Contextual analysis indicates that the bacteriophage versions of ADPr-targeting domains are more likely to counter soluble ADPr derivatives, while the eukaryotic RNA viral versions might prefer macromolecular ADPr adducts. Finally, we also use comparative genomics to predict host systems involved in countering viral ADP ribosylation of host molecules.
Primary HSV-2 Infection Complicated by Radiculomyelitis in a Young Immunocompetent Female Patient with Inherited Chromosomally Integrated HHV-6: A Case Report
Authors: Nsoga Marie Thérèse Ngo , Accorroni Alice , Mamin Aline , Schibler Manuel
Published: September 2022

Background: HSV-1, HSV-2 and VZV are alpha Herpesviruses, neurotropic viruses that are associated with various neurologic complications upon primary infection or reactivation. Cases of myelitis and radiculomyelitis are rare and appropriate etiologic diagnoses can be tricky. Case presentation: Here we describe the case of a young immunocompetent woman who developed painful and extended vesicular genital lesions, with subsequent radiculomyelitis. HSV-1/-2 PCRs in the cerebrospinal fluid were misleadingly negative, whereas HHV-6 PCR was positive. Positive anti-HSV-2 IgM and IgG in serum was consistent with HSV-2 primary infection. On the other hand, the detection of HHV-6 DNA was explained by inherited chromosomally integrated HHV-6. The clinical course was favorable with high-dose IV acyclovir and corticosteroids. Conclusion: HSV-2-related radiculomyelitis is a rare clinical entity, which can be difficult to diagnose. In this case report, the causative virus was not detected in the patient’s CSF, whereas HHV-6 DNA, non-pathogenic in this situation, was paradoxically positive. The diagnosis was based on the clinical features typical for HSV-2 primary infection, confirmed by the serology results. The delay between the genital lesions and the appearance of the radiculomyelitis, along with the absence of HSV-2 detection in the CSF, suggests a possible immuno-mediated physiopathological process. As for the HHV-6 DNA detection in the patient’s CSF, it was explained by inherited chromosomally integrated HHV-6. This case illustrates how both negative and positive clinical virology results need careful interpretation according to the clinical findings.
Forging a Functional Cure for HIV: Transcription Regulators and Inhibitors
Authors: Mediouni Sonia , Lyu Shuang , Schader Susan M. , Valente Susana T.
Published: September 2022

Current antiretroviral therapy (ART) increases the survival of HIV-infected individuals, yet it is not curative. The major barrier to finding a definitive cure for HIV is our inability to identify and eliminate long-lived cells containing the dormant provirus, termed viral reservoir. When ART is interrupted, the viral reservoir ensures heterogenous and stochastic HIV viral gene expression, which can reseed infection back to pre-ART levels. While strategies to permanently eradicate the virus have not yet provided significant success, recent work has focused on the management of this residual viral reservoir to effectively limit comorbidities associated with the ongoing viral transcription still observed during suppressive ART, as well as limit the need for daily ART. Our group has been at the forefront of exploring the viability of the block-and-lock remission approach, focused on the long-lasting epigenetic block of viral transcription such that without daily ART, there is no risk of viral rebound, transmission, or progression to AIDS. Numerous studies have reported inhibitors of both viral and host factors required for HIV transcriptional activation. Here, we highlight and review some of the latest HIV transcriptional inhibitor discoveries that may be leveraged for the clinical exploration of block-and-lock and revolutionize the way we treat HIV infections.
A Naked-Eye Visual Reverse Transcription Loop-Mediated Isothermal Amplification with Sharp Color Changes for Potential Pen-Side Test of Foot-and-Mouth Disease Virus
Authors: Zhang Jie , Hou Qian , Ma Weimin , Chen Danian , Zhang Weibing , Wubshet Ashenafi Kiros , Ding Yaozhong , Li Miaomiao , Li Qian , Chen Jiao , Dai Junfei , Wu Guohua , Zhang Ziteng , Zaberezhny Alexei D. , Pejsak Zygmunt , Tarasiuk Kazimierz , Zafar Khan Muhammad Umar , Wang Yang , He Jijun , Liu Yongsheng
Published: September 2022

Visual loop-mediated isothermal amplification (LAMP) is qualified to be applied in the field to detect pathogens due to its simplicity, rapidity and cost saving. However, the color changes in currently reported visual reverse transcription LAMP (RT-LAMP) for foot-and-mouth disease virus (FMDV) detection are not so obvious to the naked eye, so interpretation of results is troublesome. In this study, a new naked-eye visual RT-LAMP to detect all seven distinct serotypes of FMDV was established based on the 3D genes by using pH-sensitive neutral red as the indicator, rendering a sharp contrast of color changes between the negative (light orange) and the positive (pink). Analytical sensitivity tests showed that the detection limit of the visual RT-LAMP was 104 copies/µL while those were 103 and 104 copies/µL for the RT-qPCR and conventional RT-PCR methods, respectively. Specificity tests proved that the established visual RT-LAMP assay had no cross-reactivity with other common livestock viruses. Furthermore, the analysis of 59 clinical samples showed 98.31% and 100% concordance with the RT-qPCR and the RT-PCR, respectively. The pan-serotypic FMD visual RT-LAMP assay could be suitable for a pen-side test of all seven serotypes of FMDV because the results could be easily distinguished by the naked eye without the requirement of complicated instruments and professional technicians. Hence, the novel method may have a promising prospect in field tests which exert an important role in monitoring, preventing, and controlling FMD, especially in regions with no PCR or qPCR instrument available.
Bovine Herpesvirus-1 Glycoprotein M Mediates the Translocation to the Golgi Apparatus and Packaging of VP8
Authors: Sucharita Soumya , Tikoo Suresh , van Drunen Littel-van den Hurk Sylvia
Published: September 2022

VP8, the most abundant tegument protein of bovine herpesvirus-1 (BoHV-1), plays an important role in viral replication. According to our previous studies, VP8 localizes to the Golgi apparatus of BoHV-1-infected cells where it can be packaged into the virus; however, Golgi localization of VP8 does not occur outside of the context of infection. The goal of this study was to identify the viral factor(s) involved in the tropism of VP8 towards the Golgi. VP8 was found to interact with glycoprotein M (gM), and the VP8 and gM domains that are essential for this interaction were identified. VP8 and gM colocalized to the Golgi apparatus in BoHV-1-infected cells. In cells co-transfected with VP8- and gM-encoding plasmids, VP8 was also found to be localized to the Golgi, suggesting gM to be sufficient. The localization of VP8 to the Golgi was lost in cells infected with a gM deletion mutant, and the amount of VP8 incorporated into mature virus was significantly reduced. However, with the restoration of gM in a revertant virus, the localization to the Golgi and the amount of VP8 incorporated in the virions were restored. These results indicate that gM plays a critical role in VP8 subcellular localization to the Golgi and packaging into mature virions.
Heart Disease and Arboviruses: A Systematic Review and Meta-Analysis
Authors: Nicacio Jandir Mendonça , Gomes Orlando Vieira , Carmo Rodrigo Feliciano do , Nunes Sávio Luiz Pereira , Rocha José Roberto Coelho Ferreira , Souza Carlos Dornels Freire de , Franca Rafael Freitas de Oliveira , Khouri Ricardo , Barral-Netto Manoel , Armstrong Anderson da Costa
Published: September 2022

Dengue fever, chikungunya, and zika are highly prevalent arboviruses transmitted by hematophagous arthropods, with a widely neglected impact in developing countries. These diseases cause acute illness in diverse populations, as well as potential cardiovascular complications. A systematic review was carried out to investigate the burden of cardiac involvement related to these arboviruses. Multiple databases were searched for articles that investigated the association of cardiovascular diseases with arboviruses, published up to March 2022. Relevant articles were selected and rated by two independent reviewers. Proportion meta-analysis was applied to assess the frequency-weighted mean of the cardiovascular findings. A total of 42 articles were selected (n = 76,678 individuals), with 17 manuscripts on dengue and 6 manuscripts on chikungunya undergoing meta-analysis. The global pooled incidence of cardiac events in dengue fever using a meta-analysis was 27.21% (95% CI 20.21–34.83; I2 = 94%). The higher incidence of dengue-related myocarditis was found in the population younger than 20 years old (33.85%; 95% CI 0.00–89.20; I2 = 99%). Considering the studies on chikungunya (n = 372), the global pooled incidence of cardiac involvement using a meta-analysis was 32.81% (95% CI 09.58–61.49, I2 = 96%). Two Zika studies were included that examined cases of infection by vertical transmission in Brazil, finding everything from structural changes to changes in heart rate variability that increase the risk of sudden death. In conclusion, cardiac involvement in arboviruses is not uncommon, especially in dengue fever.
Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery
Authors: Pérot Philippe , Bigot Thomas , Temmam Sarah , Regnault Béatrice , Eloit Marc
Published: September 2022

We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.
Graves’ Disease Following SARS-CoV-2 Vaccination: A Systematic Review
Authors: Patrizio Armando , Ferrari Silvia Martina , Elia Giusy , Ragusa Francesca , Paparo Sabrina Rosaria , Mazzi Valeria , Antonelli Alessandro , Fallahi Poupak
Published: September 2022

(1) Background: Autoimmune diseases, including autoimmune endocrine diseases (AIED), are thought to develop following environmental exposure in patients with genetic predisposition. The vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could represent a new environmental trigger for AIED, including Graves’ disease (GD). (2) Methods: We performed a literature search of MEDLINE/PubMed databases regarding thyroid dysfunction after SARS-CoV-2 vaccination since 1 January 2020 to 31 July 2022, considering only cases of thyrotoxicosis that meet the 2016 American Thyroid Association guidelines criteria for the diagnosis of GD and arising after administration of the anti-SARS-CoV-2 vaccine, regardless of the number of doses. (3) Results: A total of 27 articles were identified, consisting of case reports or case series, of which 24 describe the appearance of 48 new diagnoses of GD and 12 GD recurrences arising after the administration of the anti-SARS-CoV-2 vaccine, and 3 papers that instead report only 3 cases of GD relapse following vaccination. (4) Conclusions: physicians should be aware of the possibility of developing GD and other autoimmune sequelae following SARS-CoV-2 vaccination. Regardless of the underlying pathogenetic mechanisms (autoimmune/inflammatory syndrome induced by adjuvants (ASIA syndrome), cytokines induction, molecular mimicry, and cross-reactivity), an individual predisposition seems to be decisive for their development.