bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal Identification of Cell Divisions Using Symmetry Properties in Time-Lapse Phase Contrast Microscopy
Authors: Hadjidemetriou Stathis , Hadjisavva Rania , Christodoulou Andri , Papageorgiou Ismini , Panayiotou Ioanna , Skourides Paris
Published: August 2022

A variety of biological and pharmaceutical studies, such as for anti-cancer drugs, require the quantification of cell responses over long periods of time. This is performed with time-lapse video microscopy that gives a long sequence of frames. For this purpose, phase contrast imaging is commonly used since it is minimally invasive. The cell responses of interest in this study are the mitotic cell divisions. Their manual measurements are tedious, subjective, and restrictive. This study introduces an automated method for these measurements. The method starts with preprocessing for restoration and reconstruction of the phase contrast time-lapse sequences. The data are first restored from intensity non-uniformities. Subsequently, the circular symmetry of the contour of the mitotic cells in phase contrast images is used by applying a Circle Hough Transform (CHT) to reconstruct the entire cells. The CHT is also enhanced with the ability to “vote” exclusively towards the center of curvature. The CHT image sequence is then registered for misplacements between successive frames. The sequence is subsequently processed to detect cell centroids in individual frames and use them as starting points to form spatiotemporal trajectories of cells along the positive as well as along the negative time directions, that is, anti-causally. The connectivities of different trajectories enhanced by the symmetry of the trajectories of the daughter cells provide as topological by-products the events of cell divisions together with the corresponding entries into mitoses as well as exits from cytokineses. The experiments use several experimental video sequences from three different cell lines with many cells undergoing mitoses and divisions. The quantitative validations of the results of the processing demonstrate the high performance and efficiency of the method.
Digitization of Manufacturing Processes: From Sensing to Twining
Authors: Stavropoulos Panagiotis
Published: August 2022

Zero-defect manufacturing and flexibility in production lines is driven from accurate Digital Twins (DT) which monitor, understand, and predict the behavior of a manufacturing process under different conditions while also adapting to them by deciding the right course of action in time intervals relevant to the captured phenomenon. During the exploration of the alternative approaches for the development of process twins, significant efforts should be made for the selection of acquisition devices and signal-processing techniques to extract meaningful information from the studied process. As such, in Industry 4.0 era, machine tools are equipped with embedded sensors that give feedback related to the process efficiency and machine health, while additional sensors are installed to capture process-related phenomena, feeding simulation tools and decision-making algorithms. Although the maturity level of some process mechanisms facilitates the representation of the physical world with the aid of physics-based models, data-driven models are proposed for complex phenomena and non-mature processes. This paper introduces the components of Digital Twin and gives emphasis on the steps that are required to transform obtained data into meaningful information that will be used in a Digital Twin. The introduced steps are identified in a case study from the milling process.
Incorporation of Metabolic Activation in the HPTLC-SOS-Umu-C Bioassay to Detect Low Levels of Genotoxic Chemicals in Food Contact Materials
Authors: Debon Emma , Rogeboz Paul , Latado Hélia , Morlock Gertrud E. , Meyer Daniel , Cottet-Fontannaz Claudine , Scholz Gabriele , Schilter Benoît , Marin-Kuan Maricel
Published: August 2022

The safety evaluation of food contact materials requires excluding mutagenicity and genotoxicity in migrates. Testing the migrates using in vitro bioassays has been proposed to address this challenge. To be fit for that purpose, bioassays must be capable of detecting very low, safety relevant concentrations of DNA-damaging substances. There is currently no bioassay compatible with such qualifications. High-performance thin-layer chromatography (HPTLC), coupled with the planar SOS Umu-C (p-Umu-C) bioassay, was suggested as a promising rapid test (~6 h) to detect the presence of low levels of mutagens/genotoxins in complex mixtures. The current study aimed at incorporating metabolic activation in this assay and testing it with a set of standard mutagens (4-nitroquinoline-N-oxide, aflatoxin B1, mitomycin C, benzo(a)pyrene, N-ethyl nitrourea, 2-nitrofluorene, 7,12-dimethylbenzanthracene, 2-aminoanthracene and methyl methanesulfonate). An effective bioactivation protocol was developed. All tested mutagens could be detected at low concentrations (0.016 to 230 ng/band, according to substances). The calculated limits of biological detection were found to be up to 1400-fold lower than those obtained with the Ames assay. These limits are lower than the values calculated to ensure a negligeable carcinogenic risk of 10−5. They are all compatible with the threshold of toxicological concern for chemicals with alerts for mutagenicity (150 ng/person). They cannot be achieved by any other currently available test procedures. The p-Umu-C bioassay may become instrumental in the genotoxicity testing of complex mixtures such as food packaging, foods, and environmental samples.
Determination of the Oxidative Stress Biomarkers of 8-Hydroxydeoxyguanosine and Dityrosine in the Gills, Skin, Dorsal Fin, and Liver Tissue of Atlantic Salmon (Salmo salar) Parr
Authors: Zhang Junjie , Sundfør Eivind B. , Klokkerengen Rolf , Gonzalez Susana V. , Mota Vasco C. , Lazado Carlo C. , Asimakopoulos Alexandros G.
Published: August 2022

Oxidative stress is a condition caused by an imbalance in the occurrence of reactive oxygen species in the cells and tissues of organisms. An ultra-performance liquid chromatography–electrospray ionization tandem mass spectrometry (UPLC–ESI–MS/MS) method was developed for the simultaneous determination of two oxidative stress biomarkers, 8-hydroxydeoxyguanosine (8OHDG) and dityrosine (DIY), in the gills, skin, dorsal fin, and liver tissue of Atlantic salmon (Salmo salar) parr. The use of target analyte-specific 13C and 15N internal standards allowed quantification of each target analyte to be performed through the standard solvent calibration curve. The relative recoveries [mean ± (relative standard deviation%)] of 8OHDG and DIY were 101 ± 11 and 104 ± 13% at a fortified concentration of 10 ng/mL (8OHDG) and 500 ng/mL (DIY), respectively, ensuring the accuracy of the extraction and quantification. The chromatographic separation was carried out using a gradient elution program with a total run time of 5 min. The limits of detection (LODs) were 0.11 and 1.37 ng/g wet weight (w.w.) for 8OHDG and DIY, respectively. To demonstrate the applicability of the developed method, it was applied in 907 tissue samples that were collected from Atlantic salmon parr individuals reared in an experimental land-based recirculating aquaculture system (RAS) treated with peracetic acid. Moreover, the possibility of using the dorsal fin as an alternative matrix for the minimally invasive assessment of oxidative stress in Atlantic salmon parr was introduced. To our knowledge, 8OHDG and DIY were used for the first time as biomarkers for biomonitoring the fish health (oxidative stress) of Atlantic salmon parr in RAS.
Juvenile Exposure to BPA Alters the Estrous Cycle and Differentially Increases Anxiety-like Behavior and Brain Gene Expression in Adult Male and Female Rats
Authors: Castillo Laura Yesenia , Ríos-Carrillo Jorge , González-Orozco Juan Carlos , Camacho-Arroyo Ignacio , Morin Jean-Pascal , Zepeda Rossana C. , Roldán-Roldán Gabriel
Published: August 2022

Perinatal exposure to bisphenol A (BPA) in murine models has been reported to affect social behavior and increase anxiety. However, there is little information about the effects of BPA exposure during puberty, a period in which sex hormones influence the maturation and differentiation of the brain. In this work, we evaluated the effect of BPA administration during the juvenile stage (PND 21–50) on anxiety in male and female rats. Newly weaned Wistar rats were treated with BPA (0, 50, or 500 µg/kg/day) for 30 days. To compare the intra- and inter-sex behavioral profiles, rats were evaluated using four different anxiety models: the Open field test (OFT), the Elevated plus maze (EPM), the Light-dark box test (LDBT), and the Defensive burying test (DBT). Males exhibited a clear-cut anxious profile at both doses in all four tests, while no clear behavioral effect of BPA exposure was observed in female rats. The latter showed an altered estrous cycle that initiated earlier in life and had a shorter duration, with the estrous phase predominating. Moreover, the expression of ESR1, ESR2, GABRA1, GRIN1, GR, MR, and AR genes increased in the hippocampus and hypothalamus of male rats treated with 50 µg/kg, but not in females. Our results indicate that BPA consistently induces a higher anxiety profile in male than in female rats, as evidenced predominantly by an increase in passive-coping behaviors and changes in brain gene expression, highlighting the importance of sex in peripubertal behavioral toxicology studies.
Poisoning Caused by Medicines and Drugs of Abuse
Authors: Bertol Elisabetta , Trignano Claudia
Published: August 2022

We believe it is necessary to state a premise on the framing of poison and poisoning in the context of Forensic Toxicology as an important contribution to this Special Issue, which is composed of articles about this discipline—the discipline of “poison” [...]
The Isolation of Specialty Compounds from Amphidinium carterae Biomass by Two-Step Solid-Phase and Liquid-Liquid Extraction
Authors: López-Rodríguez Mercedes , López-Rosales Lorenzo , Necci Giulia , Cerón-García María , Navarro-López Elvira , Gallardo-Rodríguez Juan , Tristán Ana , Abreu Ana , García-Camacho Francisco
Published: August 2022

The two main methods for partitioning crude methanolic extract from Amphidinium carterae biomass were compared. The objective was to obtain three enriched fractions containing amphidinols (APDs), carotenoids, and fatty acids. Since the most valuable bioproducts are APDs, their recovery was the principal goal. The first method consisted of a solid-phase extraction (SPE) in reverse phase that, for the first time, was optimized to fractionate organic methanolic extracts from Amphidinium carterae biomass using reverse-phase C18 as the adsorbent. The second method consisted of a two-step liquid-liquid extraction coupled with SPE and, alternatively, with solvent partitioning. The SPE method allowed the recovery of the biologically-active fraction (containing the APDs) by eluting with methanol (MeOH): water (H2O) (80:20 v/v). Alternatively, an APD purification strategy using solvent partitioning proved to be a better approach for providing APDs in a clear-cut way. When using n-butanol, APDs were obtained at a 70% concentration (w/w), whereas for the SPE method, the most concentrated fraction was only 18% (w/w). For the other fractions (carotenoids and fatty acids), a two-step liquid-liquid extraction (LLE) method coupled with the solvent partitioning method presented the best results.
Effect of Nitrogen, Phosphorous, and Light Colimitation on Amphidinol Production and Growth in the Marine Dinoflagellate Microalga Amphidinium carterae
Authors: Molina-Miras Alejandro , Bueso-Sánchez Alejandro , Cerón-García María del Carmen , Sánchez-Mirón Asterio , Contreras-Gómez Antonio , García-Camacho Francisco
Published: August 2022

The marine dinoflagellate microalga Amphidinium carterae is a source of amphidinols, a fascinating group of polyketide metabolites potentially useful in drug design. However, Amphidinium carterae grows slowly and produces these toxins in tiny amounts, representing a hurdle for large-scale production. Understanding dinoflagellate growth kinetics under different photobioreactor conditions is imperative for promoting the successful implementation of a full-scale integrated bioproduct production system. This study evaluates the feasibility of growing Amphidinium carterae under different ranges of nitrogen concentration (NO3− = 882–2646 µM), phosphorus concentration (PO33− = 181–529 µM), and light intensity (Y0 = 286–573 µE m−2 s−1) to produce amphidinols. A mathematical colimitation kinetic model based on the “cell quota” concept is developed to predict both algal growth and nutrient drawdown, assuming that all three variables (nitrogen, phosphorous and light) can simultaneously colimit microalgal growth. The model was applied to the semicontinuous culture of the marine microalgae Amphidinium carterae in an indoor LED-lit raceway photobioreactor. The results show that both growth and amphidinol production strongly depend on nutrient concentrations and light intensity. Nonetheless, it was possible to increase Amphidinium carterae growth while simultaneously promoting the overproduction of amphidinols. The proposed model adequately describes Amphidinium carterae growth, nitrate and phosphate concentrations, and intracellular nitrogen and phosphorus storage, and has therefore the potential to be extended to other systems used in dinoflagellate cultivation and the production of bioproducts obtained therein.
Histopathological Changes in the Liver, Heart and Kidneys Following Malayan Pit Viper (Calloselasma rhodostoma) Envenoming and the Neutralising Effects of Hemato Polyvalent Snake Antivenom
Authors: Khimmaktong Wipapan , Nuanyaem Nazmi , Lorthong Nissara , Hodgson Wayne C. , Chaisakul Janeyuth
Published: August 2022

Calloselasma rhodostoma (Malayan pit viper) is a medically important snake species that is widely distributed across Southeast Asia. Systemic coagulopathy causing severe haemorrhage and local tissue injury is commonly observed following C. rhodostoma envenoming. However, nephrotoxicity and congestive heart failure were previously reported in a patient who had a long length of hospital stay. In this study, we determined the effect of C. rhodostoma envenoming on cardiovascular disturbances and the associated morphological changes in the liver, heart and kidneys using animal models. We also evaluated the efficacy of Hemato polyvalent antivenom (HPAV; Queen Saovabha Memorial Institute (QSMI) of the Thai Red Cross Society, Thailand) in neutralising the histopathological effects of C. rhodostoma venom. The intravenous (i.v.) administration of C. rhodostoma venom (1000 µg/kg) caused a rapid decrease in mean arterial pressure (MAP) followed by complete cardiac collapse in anaesthetized rats. Moreover, the intraperitoneal (i.p.) administration of C. rhodostoma venom (11.1 mg/kg; 3 × LD50) for 24 h caused cellular lesions in the liver and heart tissues. C. rhodostoma venom also induced nephrotoxicity, as indicated by the presence of tubular injury, interstitial vascular congestion and inflammatory infiltration in the whole area of the kidney. The administration of HPAV, at manufacturer-recommended doses, 15 min prior to or after the addition of C. rhodostoma venom reduced the extent of the morphological changes in the liver, heart and kidneys. This study found that experimental C. rhodostoma envenoming induced cardiovascular disturbances, hepatotoxicity and nephrotoxicity. We also highlighted the potential broad utility of HPAV to neutralise the histopathological effects of C. rhodostoma venom. The early delivery of antivenom appears capable of preventing envenoming outcomes.
The Lanczos Potential for Bianchi Spacetime
Authors: Roberts Mark D.
Published: August 2022

The form and application of the Lanczos potential for Bianchi spacetime are studied. The Lanczos potential is found in some specific cases, then the general case is studied. It leads to two coupled first order partial differential equations which, although they so far have not been solved in general, can be solved for many configurations. The application is to cosmic energetics: in other words to the study of the energy of the gravitational and other fields in the Universe.
Gravitational Waves from Strange Star Core–Crust Oscillation
Authors: Zou Ze-Cheng , Huang Yong-Feng , Zhang Xiao-Li
Published: August 2022

According to the strange quark matter hypothesis, pulsars may actually be strange stars composed of self-bound strange quark matter. The normal matter crust of a strange star, unlike that of a normal neutron star, is supported by a strong electric field. A gap is then presented between the crust and the strange quark core. Therefore, peculiar core–crust oscillation may occur in a strange star, which can produce distinctive gravitational waves. In this paper, the waveforms of such gravitational waves are derived using a rigid model. We find that the gravitational waves are extremely weak and undetectable, even for the next-generation detectors. Therefore, the seismology of a strange star is not affected by the core–crust oscillation. Observers will have to search for other effects to diagnose the existence of the crust.
Noncommutative Reduction of Nonlinear Schrödinger Equation on Lie Groups
Authors: Breev Alexander , Shapovalov Alexander , Gitman Dmitry
Published: August 2022

We propose a new approach that allows one to reduce nonlinear equations on Lie groups to equations with a fewer number of independent variables for finding particular solutions of the nonlinear equations. The main idea is to apply the method of noncommutative integration to the linear part of a nonlinear equation, which allows one to find bases in the space of solutions of linear partial differential equations with a set of noncommuting symmetry operators. The approach is implemented for the generalized nonlinear Schrödinger equation on a Lie group in curved space with local cubic nonlinearity. General formalism is illustrated by the example of the noncommutative reduction of the nonstationary nonlinear Schrödinger equation on the motion group E(2) of the two-dimensional plane R2. In this particular case, we come to the usual (1+1)-dimensional nonlinear Schrödinger equation with the soliton solution. Another example provides the noncommutative reduction of the stationary multidimensional nonlinear Schrödinger equation on the four-dimensional exponential solvable group.
Calculation of the Cosmological Constant for the Planetary System in Schwarzschild’s Cosmological Model
Authors: Salas Salas Alvaro Humberto , Castillo Hernandez Jairo Ernesto , Pinzon Quintero Jorge Enrique
Published: August 2022

In this work, the static cosmological model of the Schwarzschild solution for the solar system is proposed taking into account the cosmological constant in the equation of the general theory of relativity (GTR) proposed by A. Einstein. We found the nonlinear differential equation that describes the behavior of the planets around the Sun; this is solved exactly by the Jacobi and Weierstrass elliptic functions. The obtained solution allows for us to estimate the value of the cosmological constant knowing the perihelion of the different planets and from different mathematical approaches; that is, the inverse problem is solved. From the obtained results, the Schwarzschild static cosmological model for the solar system is proposed, establishing the Schwarzschild cosmological radius and the curvature limit of the solar system. From the curvature limit, different regions are proposed for the planets, exoplanets, and a region is predicted where the existence of new planets and exoplanets belonging to the solar system is possible. The proposed theory of the static Schwarzschild cosmological model may be of great interest to astronomers, cosmologists, and all those interested in the study of the universe.
Analogue Non-Causal Null Curves and Chronology Protection in a dc-SQUID Array
Authors: Sabín Carlos
Published: August 2022

We propose an analogue quantum simulator of a 1 + 1D spacetime containing non-causal curves, in particular null geodesics going back in time, by means of a dc-SQUID array embedded on an open superconducting transmission line. This is achieved by mimicking the spatial dependence of the metric with the propagation speed of the electromagnetic field in the simulator, which can be modulated by an external magnetic flux. We show that it is possible to simulate a spacetime region containing non-causal null geodesics, but not a full spacetime containing a chronological horizon separating regions with non-causal null geodesics and regions without them. This is in agreement with a recent suggestion of an analogue-gravity chronology protection mechanism by Barceló et al.
Hunting Quantum Gravity with Analogs: The Case of Graphene
Authors: Acquaviva Giovanni , Iorio Alfredo , Pais Pablo , Smaldone Luca
Published: August 2022

Analogs of fundamental physical phenomena can be used in two ways. One way consists in reproducing specific aspects of the classical or quantum gravity of quantum fields in curved space or of other high-energy scenarios on lower-energy corresponding systems. The “reverse way” consists in building fundamental physical theories, for instance, quantum gravity models, inspired by the lower-energy corresponding systems. Here, we present the case of graphene and other Dirac materials.
Selection and Characterization of Single-Stranded DNA Aptamers of Diagnostic Potential against the Whole Zika Virus
Authors: Morais Liliane Monteiro de , Chaves Thiago Santos , Medeiros Marco Alberto , Pereira Kaique Alves Brayner , Jurgilas Patrícia Barbosa , Barbosa de Lima Sheila Maria , Missailidis Sotiris , Bispo de Filippis Ana Maria
Published: August 2022

Zika virus became a major public health problem in early 2015, when cases of Guillain–Barré syndrome and microcephaly were associated with viral infection. Currently, ZIKV is endemic in all tropical areas of the world, and the chance for future Zika epidemics remains very real and accurate diagnosis is crucial. The aim of this work was to select specific ssDNA aptamers that bind to the entire Zika virus and can be used to compose specific diagnostics, without cross-reactivity with other flaviviruses. Zika virus was cultivated in Vero cells and used as a target for aptamer selection. Aptamers specific for the ZIKV were selected using whole-virus SELEX, with counterselection for other flavivirus. Secondary and tertiary structures were evaluated and the molecular anchoring between the aptamers and target were simulated by the HDOCK server. Aptamer interaction was evaluated by ELISA/ELASA and the dissociation constant (Kd) was calculated by thermophoresis. Four ZIKV-specific aptamers were selected. The best two were further characterized and proved to be specific for ZIKV. Aptamers are capable of binding specifically to the ZIKV and differentiate from Dengue virus. The aptamers selected in this work can be used as capture agents in the composition of diagnostic tests to specifically detect ZIKV infection.
Sacbrood Virus: A Growing Threat to Honeybees and Wild Pollinators
Authors: Wei Ruike , Cao Lianfei , Feng Ye , Chen Yanping , Chen Gongwen , Zheng Huoqing
Published: August 2022

Sacbrood virus (SBV) is one of the many viruses that infect both the Western honeybee (Apis mellifera) and the Eastern honeybee (Apis cerana). Recently, the interspecies transmission of SBV has been discovered, especially among wild pollinators. This newly discovered evolutionary occurrence regarding SBV indicates a much wider host range than previously believed, causing further concern about the future sustainability of agriculture and the resilience of ecosystems. Over the past few decades, vast numbers of studies have been undertaken concerning SBV infection in honeybees, and remarkable progress has been made in our understanding of the epidemiology, pathogenesis, transmission, and manifestations of SBV infection in honeybees and other pollinators. Meanwhile, some methods, including Chinese medicine, have been established to control and prevent sacbrood disease in A. cerana in Asian countries. In this review, we summarize the existing knowledge of SBV and address the gaps in the knowledge within the existing literature in the hope of providing future directions for the research and development of management strategies for controlling the spread of this deadly disease.
Identification of Equine Arteritis Virus Immunodominant Epitopes Using a Peptide Microarray
Authors: Mayers Jo , Westcott David , Steinbach Falko
Published: August 2022

Using the commercially available PEPperCHIP® microarray platform, a peptide microarray was developed to identify immunodominant epitopes for the detection of antibodies against Equine arteritis virus (EAV). For this purpose, the whole EAV Bucyrus sequence was used to design a total of 1250 peptides that were synthesized and spotted onto a microarray slide. A panel of 28 serum samples representing a selection of EAV strains was tested using the microarray. Of the 1250 peptides, 97 peptides (7.76%) showed reactivity with the EAV-positive samples. No single peptide was detected by all the positive serum samples. Seven peptides repeatedly showed reactivity above the cut-off and were considered to have diagnostic potential. Five of these peptides were within the immunodominant GP5 protein and two were within the replicase polyprotein regions NSP2 and NSP10, located in ORF1. The diagnostic sensitivity of the seven peptides selected was low, ranging from 5% to 55%; however, the combined diagnostic sensitivity and specificity of the seven peptides was 90% and 100%, respectively. This data demonstrate that multiple peptide sequences would be required to design a comprehensive serological test to cover the diversity of the EAV strains and the individual immune responses of horses.
Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management
Authors: Diouf Mame Boucar , Festus Ruth , Silva Gonçalo , Guyader Sébastien , Umber Marie , Seal Susan , Teycheney Pierre Yves
Published: August 2022

Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.
Predictable Chikungunya Infection Dynamics in Brazil
Authors: Yakob Laith
Published: August 2022

Chikungunya virus (CHIKV) was first imported into the Caribbean in 2013 and subsequently spread across the Americas. It has infected millions in the region and Brazil has become the hub of ongoing transmission. Using Seasonal Autoregressive Integrated Moving Average (SARIMA) models trained and validated on Brazilian data from the Ministry of Health’s notifiable diseases information system, we tested the hypothesis that transmission in Brazil had transitioned from sporadic and explosive to become more predictable. Consistency weighted, population standardized kernel density estimates were used to identify municipalities with the most consistent inter-annual transmission rates. Spatial clustering was assessed per calendar month for 2017–2021 inclusive using Moran’s I. SARIMA models were validated on 2020–2021 data and forecasted 106,162 (95%CI 27,303–200,917) serologically confirmed cases and 339,907 (95%CI 35,780–1035,449) total notifications for 2022–2023 inclusive, with >90% of cases in the Northeast and Southeast regions. Comparing forecasts for the first five months of 2022 to the most up-to-date ECDC report (published 2 June 2022) showed remarkable accuracy: the models predicted 92,739 (95%CI 20,685–195,191) case notifications during which the ECDC reported 92,349 case notifications. Hotspots of consistent transmission were identified in the states of Para and Tocantins (North region); Rio Grande do Norte, Paraiba and Pernambuco (Northeast region); and Rio de Janeiro and eastern Minas Gerais (Southeast region). Significant spatial clustering peaked during late summer/early autumn. This analysis highlights how CHIKV transmission in Brazil has transitioned, making it more predictable and thus enabling improved control targeting and site selection for trialing interventions.
Undiagnosed HIV Infections May Drive HIV Transmission in the Era of “Treat All”: A Deep-Sampling Molecular Network Study in Northeast China during 2016 to 2019
Authors: Zhao Bin , Qiu Yu , Song Wei , Kang Mingming , Dong Xue , Li Xin , Wang Lu , Liu Jianmin , Ding Haibo , Chu Zhenxing , Wang Lin , Tian Wen , Shang Hong , Han Xiaoxu
Published: August 2022

Universal antiretroviral therapy (ART, “treat all”) was recommended by the World Health Organization in 2015; however, HIV-1 transmission is still ongoing. This study characterizes the drivers of HIV transmission in the “treat all” era. Demographic and clinical information and HIV pol gene were collected from all newly diagnosed cases in Shenyang, the largest city in Northeast China, during 2016 to 2019. Molecular networks were constructed based on genetic distance and logistic regression analysis was used to assess potential transmission source characteristics. The cumulative ART coverage in Shenyang increased significantly from 77.0% (485/630) in 2016 to 93.0% (2598/2794) in 2019 (p < 0.001). Molecular networks showed that recent HIV infections linked to untreated individuals decreased from 61.6% in 2017 to 28.9% in 2019, while linking to individuals with viral suppression (VS) increased from 9.0% to 49.0% during the same time frame (p < 0.001). Undiagnosed people living with HIV (PLWH) hidden behind the links between index cases and individuals with VS were likely to be male, younger than 25 years of age, with Manchu nationality (p < 0.05). HIV transmission has declined significantly in the era of “treat all”. Undiagnosed PLWH may drive HIV transmission and should be the target for early detection and intervention.
Detection and Characterization of a Reassortant Mammalian Orthoreovirus Isolated from Bats in Xinjiang, China
Authors: Yan Xiaomin , Sheng Jinliang , Zhang Chang , Li Nan , Yi Le , Zhao Zihan , Feng Ye , Tu Changchun , He Biao
Published: August 2022

Mammalian orthoreoviruses (MRVs) are increasingly reported to cause various diseases in humans and other animals, with many possibly originating from bats, highlighting the urgent need to investigate the diversity of bat-borne MRVs (BtMRVs). Here, we report the detection and characterization of a reassortant MRV that was isolated from a bat colony in Xinjiang, China. The BtMRV showed a wide host and organ tropism and can efficiently propagate the cell lines of different animals. It caused mild damage in the lungs of the experimentally inoculated suckling mice and was able to replicate in multiple organs for up to three weeks post-inoculation. Complete genome analyses showed that the virus was closely related to MRVs in a wide range of animals. An intricate reassortment network was revealed between the BtMRV and MRVs of human, deer, cattle, civet and other bat species. Specifically, we found a bat-specific clade of segment M1 that provides a gene source for the reassortment of human MRVs. These data provide important insights to understand the diversity of MRVs and their natural circulation between bats, humans, and other animals. Further investigation and surveillance of MRV in bats and other animals are needed to control and prevent potential MRV-related diseases.
Emergence of a Reassortant 2.3.4.4b Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021
Authors: Ouoba Lalidia Bruno , Habibata-Zerbo Lamouni , Zecchin Bianca , Barbierato Giacomo , Hamidou-Ouandaogo Sandaogo , Palumbo Elisa , Giussani Edoardo , Bortolami Alessio , Niang Mamadou , Traore-Kam Adele , Terregino Calogero , Guitti-Kindo Mariétou , Angot Angelique , Guigma Dominique , Barro Nicolas , Fusaro Alice , Monne Isabella
Published: August 2022

Since 2006, the poultry population in Burkina Faso has been seriously hit by different waves of Highly Pathogenic Avian Influenza (HPAI) H5N1 epizootics. In December 2021, three distinct regions of Burkina Faso, namely, Gomboussougou, Bonyollo, and Koubri, detected HPAI H5N1 viruses in poultry. Whole genome characterization and statistical phylogenetic approaches were applied to shed light on the potential origin of these viruses and estimate the time of virus emergence. Our results revealed that the HPAI H5N1 viruses reported in the three affected regions of Burkina Faso cluster together within clade 2.3.4.4b, and are closely related to HPAI H5N1 viruses identified in Nigeria and Niger in the period 2021–2022, except for the PA gene, which clusters with H9N2 viruses of the zoonotic G1 lineage collected in West Africa between 2017 and 2020. These reassortant viruses possess several mutations that may be associated with an increased zoonotic potential. Although it is difficult to ascertain where and when the reassortment event occurred, the emergence of a H5N1/H9N2 reassortant virus in a vulnerable region, such as West Africa, raises concerns about its possible impact on animal and human health. These findings also highlight the risk that West Africa may become a new hotspot for the emergence of new genotypes of HPAI viruses.
Synthetic gRNA/Cas9 Ribonucleoprotein Inhibits HIV Reactivation and Replication
Authors: Khanal Sushant , Cao Dechao , Zhang Jinyu , Zhang Yi , Schank Madison , Dang Xindi , Nguyen Lam Ngoc Thao , Wu Xiao Y. , Jiang Yong , Ning Shunbin , Zhao Juan , Wang Ling , Gazzar Mohamed El , Moorman Jonathan P. , Yao Zhi Q.
Published: August 2022

The current antiretroviral therapy (ART) for human immunodeficiency virus (HIV) can halt viral replication but cannot eradicate HIV infection because proviral DNA integrated into the host genome remains genetically silent in reservoir cells and is replication-competent upon interruption or cessation of ART. CRISPR/Cas9-based technology is widely used to edit target genes via mutagenesis (i.e., nucleotide insertion/deletion and/or substitution) and thus can inactivate integrated proviral DNA. However, CRISPR/Cas9 delivery systems often require viral vectors, which pose safety concerns for therapeutic applications in humans. In this study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a non-viral formulation to develop a novel HIV gene therapy. We designed a series of gRNAs targeting different HIV genes crucial for HIV replication and tested their antiviral efficacy and cellular cytotoxicity in lymphoid and monocytic latent HIV cell lines. Compared with the scramble gRNA control, HIV-gRNA/Cas9 RNP-treated cells exhibited efficient viral suppression with no apparent cytotoxicity, as evidenced by the significant inhibition of latent HIV DNA reactivation and RNA replication. Moreover, HIV-gRNA/Cas9 RNP inhibited p24 antigen expression, suppressed infectious viral particle production, and generated specific DNA cleavages in the targeted HIV genes that are confirmed by DNA sequencing. Because of its rapid DNA cleavage, low off-target effects, low risk of insertional mutagenesis, easy production, and readiness for use in clinical application, this study provides a proof-of-concept that synthetic gRNA/Cas9 RNP drugs can be utilized as a novel therapeutic approach for HIV eradication.
CAPG Is Required for Ebola Virus Infection by Controlling Virus Egress from Infected Cells
Authors: Mori Hiroyuki , Connell James P. , Donahue Callie J. , Boytz RuthMabel , Nguyen Yen Thi Kim , Leung Daisy W. , LaCount Douglas J. , Davey Robert A.
Published: August 2022

The replication of Ebola virus (EBOV) is dependent upon actin functionality, especially at cell entry through macropinocytosis and at release of virus from cells. Previously, major actin-regulatory factors involved in actin nucleation, such as Rac1 and Arp2/3, were shown important in both steps. However, downstream of nucleation, many other cell factors are needed to control actin dynamics. How these regulate EBOV infection remains largely unclear. Here, we identified the actin-regulating protein, CAPG, as important for EBOV replication. Notably, knockdown of CAPG specifically inhibited viral infectivity and yield of infectious particles. Cell-based mechanistic analysis revealed a requirement of CAPG for virus production from infected cells. Proximity ligation and split-green fluorescent protein reconstitution assays revealed strong association of CAPG with VP40 that was mediated through the S1 domain of CAPG. Overall, CAPG is a novel host factor regulating EBOV infection through connecting actin filament stabilization to viral egress from cells.
The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications
Authors: Zhang Menghui , Zhang Tianyou , Yu Meishun , Chen Yu-Lei , Jin Min
Published: August 2022

Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles.
Heterogenous CD8+ T Cell Maturation and ‘Polarization’ in Acute and Convalescent COVID-19 Patients
Authors: Kudryavtsev Igor V. , Arsentieva Natalia A. , Korobova Zoia R. , Isakov Dmitry V. , Rubinstein Artem A. , Batsunov Oleg K. , Khamitova Irina V. , Kuznetsova Raisa N. , Savin Tikhon V. , Akisheva Tatiana V. , Stanevich Oksana V. , Lebedeva Aleksandra A. , Vorobyov Evgeny A. , Vorobyova Snejana V. , Kulikov Alexander N. , Sharapova Maria A. , Pevtsov Dmitrii E. , Totolian Areg A.
Published: August 2022

Background. The adaptive antiviral immune response requires interaction between CD8+ T cells, dendritic cells, and Th1 cells for controlling SARS-CoV-2 infection, but the data regarding the role of CD8+ T cells in the acute phase of COVID-19 and post-COVID-19 syndrome are still limited. Methods.. Peripheral blood samples collected from patients with acute COVID-19 (n = 71), convalescent subjects bearing serum SARS-CoV-2 N-protein-specific IgG antibodies (n = 51), and healthy volunteers with no detectable antibodies to any SARS-CoV-2 proteins (HC, n = 46) were analyzed using 10-color flow cytometry. Results. Patients with acute COVID-19 vs. HC and COVID-19 convalescents showed decreased absolute numbers of CD8+ T cells, whereas the frequency of CM and TEMRA CD8+ T cells in acute COVID-19 vs. HC was elevated. COVID-19 convalescents vs. HC had increased naïve and CM cells, whereas TEMRA cells were decreased compared to HC. Cell-surface CD57 was highly expressed by the majority of CD8+ T cells subsets during acute COVID-19, but convalescents had increased CD57 on ‘naïve’, CM, EM4, and pE1 2–3 months post-symptom onset. CXCR5 expression was altered in acute and convalescent COVID-19 subjects, whereas the frequencies of CXCR3+ and CCR4+ cells were decreased in both patient groups vs. HC. COVID-19 convalescents had increased CCR6-expressing CD8+ T cells. Moreover, CXCR3+CCR6- Tc1 cells were decreased in patients with acute COVID-19 and COVID-19 convalescents, whereas Tc2 and Tc17 levels were increased compared to HC. Finally, IL-27 negatively correlated with the CCR6+ cells in acute COVID-19 patients. Conclusions. We described an abnormal CD8+ T cell profile in COVID-19 convalescents, which resulted in lower frequencies of effector subsets (TEMRA and Tc1), higher senescent state (upregulated CD57 on ‘naïve’ and memory cells), and higher frequencies of CD8+ T cell subsets expressing lung tissue and mucosal tissue homing molecules (Tc2, Tc17, and Tc17.1). Thus, our data indicate that COVID-19 can impact the long-term CD8+ T cell immune response.
Integrated Jingmenvirus Polymerase Gene in Ixodes ricinus Genome
Authors: Morozkin Evgeny S. , Makenov Marat T. , Zhurenkova Olga B. , Kholodilov Ivan S. , Belova Oxana A. , Radyuk Ekaterina V. , Fyodorova Marina V. , Grigoreva Yana E. , Litov Alexander G. , Valdokhina Anna V. , Bulanenko Victoria P. , Samoilov Andrei E. , Korneenko Elena V. , Voizekhovskaya Yana A. , Neverov Alexey D. , Karganova Galina G. , Karan Lyudmila S.
Published: August 2022

Members of the jingmenviruses group have been found in arthropods and mammals on all continents except Australia and Antarctica. Two viruses of this group were isolated from patients with fever after a tick bite. Using a nested RT-PCR assay targeting a jingmenvirus polymerase gene fragment, we screened ticks collected in seven regions of Russia and found that the abundant jingmenvirus-positive were of Ixodes ricinus species, with the prevalence ranging from 19.8% to 34.3%. In all cases, DNase/RNase treatment suggested that the detected molecule was DNA and subsequent next generation sequencing (NGS) proved that the viral polymerase gene was integrated in the I. ricinus genome. The copy number of the integrated polymerase gene was quantified by qPCR relative to the ITS2 gene and estimated as 1.32 copies per cell. At least three different genetic variants of the integrated polymerase gene were found in the territory of Russia. Phylogenetic analysis of the integrated jingmenvirus polymerase gene showed the highest similarity with the sequence of the correspondent gene obtained in Serbia from I. ricinus.
Protective Immunity of COVID-19 Vaccination with ChAdOx1 nCoV-19 Following Previous SARS-CoV-2 Infection: A Humoral and Cellular Investigation
Authors: Azamor Tamiris , Horbach Ingrid Siciliano , Brito e Cunha Danielle , Melgaço Juliana Gil , Silva Andréa Marques Vieira da , Tubarão Luciana Neves , Azevedo Adriana de Souza , Santos Renata Tourinho , Alves Nathalia dos Santos , Machado Thiago Lazari , Silva Jane , Souza Alessandro Fonseca de , Bayma Camilla , Rocha Vanessa Pimenta , Frederico Ana Beatriz Teixeira , Dias Brenda de Moura , Setatino Bruno Pimenta , Denani Caio Bidueira , Campos Samir Pereira da Costa , Schwarcz Waleska Dias , Sucupira Michel Vergne , Mendes Edinea Pastro , Silva Edimilson Domingos da , Barbosa de Lima Sheila Maria , Ano Bom Ana Paula Dinis , Missailidis Sotiris
Published: August 2022

Infections caused by SARS-CoV-2 induce a severe acute respiratory syndrome called COVID-19 and have led to more than six million deaths worldwide. Vaccination is the most effective preventative measure, and cellular and humoral immunity is crucial to developing individual protection. Here, we aim to investigate hybrid immunity against SARS-CoV-2 triggered by the ChAadOx1 nCoV-19 vaccine in a Brazilian cohort. We investigated the immune response from ChAadOx1 nCoV-19 vaccination in naïve (noCOVID-19) and previously infected individuals (COVID-19) by analyzing levels of D-dimers, total IgG, neutralizing antibodies (Nabs), IFN-γ (interferon-γ) secretion, and immunophenotyping of memory lymphocytes. No significant differences in D-dimer levels were observed 7 or 15 days after vaccination (DAV). All vaccinated individuals presented higher levels of total IgG or Nabs with a positive correlation (R = 0.88). Individuals in the COVID-19 group showed higher levels of antibody and memory B cells, with a faster antibody response starting at 7 DAV compared to noCOVID-19 at 15 DAV. Further, ChAadOx1 nCoV-19 vaccination led to enhanced IFN-γ production (15 DAV) and an increase in activated T CD4+ naïve cells in noCOVID-19 individuals in contrast with COVID-19 individuals. Hence, our data support that hybrid immunity triggered by ChAadOx1 nCoV-19 vaccination is associated with enhanced humoral response, together with a balanced cellular response.
Cortical Auditory Evoked Potentials in Children with Prenatal Exposure to Zika Virus
Authors: da Hora Laís Cristine Delgado , Muniz Lilian Ferreira , Venâncio Leonardo Gleygson Angelo , Advíncula Karina Paes , da Silva Jéssica Dayane , de Albuquerque Britto Diana Babini Lapa , de Barros Miranda Filho Demócrito , Brickley Elizabeth B. , de Alencar Ximenes Ricardo Arraes , da Silva Caldas Neto Silvio , de Carvalho Leal Mariana
Published: August 2022

Prenatal exposure to ZIKV can cause neurologic and auditory damage. The electrophysiological responses obtained by Cortical Auditory Evoked Potentials (CAEP) may provide an objective method to investigate the function of cortical auditory pathways in children exposed to ZIKV. This case series analyzed the findings of CAEP in prenatal-period ZIKV-exposed children with and without microcephaly. The CAEP was performed in a total of 24 children. Five magnetic resonance imaging (MRI) images of the inner ear and brain of microcephalic children were analyzed and compared with CAEP measurements. Ventriculomegaly (80%), cortical/subcortical calcification (80%), and brain reduction (60%) were the most common alterations in the MRI. The P1-N1-P2 complex of the CAEP was observed in all children evaluated. The peak N2 was absent in two children. In the comparison of the CAEP measurements between the groups, children with microcephaly presented a higher amplitude of P2 (p = 0.017), which may reflect immaturity of the auditory pathways. Microcephalic and normocephalic children with prenatal exposure to ZIKV presented with the mandatory components of the CAEPs, regardless of changes in the CNS, suggesting that this population has, to some extent, the cortical ability to process sound stimuli preserved.
Implementation of Novel Quality Assurance Program for Hepatitis C Viral Load Point of Care Testing
Authors: Dimech Wayne , Cabuang Liza , Davies Kylie , Vincini Giuseppe
Published: August 2022

All patients should have access to accurate and timely test results. The introduction of point of care testing (PoCT) for infectious diseases has facilitated access to those unable to access traditional laboratory-based medical testing, including those living in remote and regional locations, or individuals who are marginalized or incarcerated individuals. In many countries, laboratory testing for infectious diseases, such as hepatitis C virus (HCV), is performed in a highly regulated environment. However, this is not the case for PoCT, where testing is performed by non-laboratory staff and quality controls are often lacking. An assessment of the provision of laboratory-based quality assurance to PoCT for infectious disease was conducted and the barriers to participation identified. A novel approach to providing quality assurance to PoCT sites, in particular those testing for HCV, was designed and piloted. This novel approach incudes identifying and validating sample types that are inactivated and stable at ambient temperature, creating cost-effective supply chains to facilitate logistics of samples, and the development of a smart phone-enabled portal for data entry and analyses. The creation and validation of this approach to quality assurance of PoCT removes the barriers to participation and acts to improve the quality and accuracy of testing, reduce errors and waste, and improve patient outcomes.