bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Event-Triggered Integral Sliding Mode Adaptive Optimal Tracking Control for Uncertain Nonlinear Systems
Authors: Tan Wei , Yu Wenwu , Wang He
Published: June 2022

In this paper, we study the event-triggered integral sliding mode optimal tracking problem of nonlinear systems with matched and unmatched disturbances. The goal is to design an adaptive dynamic programming-based sliding-mode controller, which stabilizes the closed-loop system and guarantees the optimal performance of the sliding-mode dynamics. First, in order to remove the effects of the matched uncertainties, an event-triggered sliding mode controller is designed to force the state of the systems on the sliding mode surface without Zeno behavior. Second, another event-triggered controller is designed to suppress unmatched disturbances with a nearly optimal performance while also guaranteeing Zeno-free behavior. Finally, the benefits of the proposed algorithm are shown in comparison to several traditional triggering and learning-based mechanisms.
New Approach to Cross-Correlation Reflectometry Diagnostics of Nonlocality of Plasma Turbulence
Authors: Kukushkin Alexander B. , Kulichenko Andrei A.
Published: June 2022

One of the most important properties of stochastic nonlinear processes, including the turbulence of the hydrodynamic motion of continuous media, is distant spatial correlations. To describe them, an approach was proposed by Shlesinger and colleagues based on a linear integro-differential equation with a slowly decaying kernel, which corresponds to superdiffusion (nonlocal) transfer in the regime of Lévy walks (Lévy flights when the finite velocity of the carriers is taken into account). In this paper, we formulate a similar approach that makes it possible to formulate the problem of determining these properties from the scattering spectra of electromagnetic (EM) waves and cross-correlation reflectometry. A universal description of the relationship between the observed symmetric quasi-coherent component in the spectrum of scattered EM waves in plasmas and a process of the Mandelstam–Brillouin scattering type is obtained. It is shown that the nonlocality of spatial correlations of density fluctuations in a turbulent medium is due to long-free-path carriers of the medium’s perturbations, for which the free path distribution function is described by the Lévy distribution. The effectiveness of the proposed method is shown by the example of the interpretation of the data of cross-correlation reflectometry of EM waves in the radio-frequency range for the diagnosis of turbulent plasma in magnetic confinement devices for axisymmetric toroidal thermonuclear plasma.
Deep-Learning-Based Floor Path Model for Route Tracking of Autonomous Vehicles
Authors: Erginli Mustafa , Cil Ibrahim
Published: June 2022

Real-time route tracking is an important research topic for autonomous vehicles used in industrial facilities. Traditional methods such as copper line tracking on the ground, wireless guidance systems, and laser systems are still used in route tracking. In this study, a deep-learning-based floor path model for route tracking of autonomous vehicles is proposed. A deep-learning floor path model and algorithm have been developed for highly accurate route tracking, which avoids collisions of vehicles and follows the shortest route to reach the destination. The floor path model consists of markers. Routes in the floor path model are created by using these markers. The floor path model is transmitted to autonomous vehicles as a vector by a central server. The server dispatches the target marker address to the vehicle to move. The vehicle calculates all possible routes to this address and chooses the shortest one. Marker images on the selected route are processed using image processing and classified with a pre-trained deep-CNN model. If the classified image and the image on the selected route are the same, the vehicle proceeds toward its destination. While the vehicle moves on the route, it sends the last classified marker to the server. Other autonomous vehicles use this marker to determine the location of this vehicle. Other vehicles on the route wait to avoid a collision. As a result of the experimental studies we have carried out, the route tracking of the vehicles has been successfully achieved.
Short-Term Associations between PM10 and Respiratory Health Effects in Visby, Sweden
Authors: Tornevi Andreas , Olstrup Henrik , Forsberg Bertil
Published: June 2022

The old Swedish city Visby, located on the island Gotland, has, for several years, reported higher PM10 concentrations than any other city in Sweden. In Visby, local limestone is used, both in road paving and as sand used for anti-slip measures, resulting in a clear annual pattern of PM10 with the highest concentrations during winter/spring when studded tires are allowed. This study analyzes the short-term associations between PM10 and daily number of patients with acute respiratory problems (ICD–10 diagnoses: J00–J99) seeking care at the hospital or primary healthcare units in Visby during the period of 2013–2019. The daily mean of PM10 was on average 45 µg m−3 during winter/spring and 18 µg m−3 during summer/autumn. Four outcome categories were analyzed using quasi-Poisson regression models, stratifying for period and adjusting for calendar variables and weather. An increase in respiratory visits was associated with increasing concentrations in PM10 during the summer/autumn period, most prominent among children, where asthma visits increased by 5% (95% CI: 2–9%) per 10 µg m−3 increase in PM10. For the winter/spring period, no significant effects were observed, except for the diagnose group ‘upper airways’ in adults, where respiratory visits increased by 1% (95% CI: 0.1–1.9%) per 10 µg m−3 increase. According to the results, limestone in particles seem to be relatively harmless at the exposure concentrations observed in Visby, and this is in line with the results from a few experimental and occupational studies.
Multi- and Transgenerational Effects of Developmental Exposure to Environmental Levels of PFAS and PFAS Mixture in Zebrafish (Danio rerio)
Authors: Haimbaugh Alex , Wu Chia-Chen , Akemann Camille , Meyer Danielle N. , Connell Mackenzie , Abdi Mohammad , Khalaf Aicha , Johnson Destiny , Baker Tracie R.
Published: June 2022

Per- and polyfluoroalkyl substances (PFASs) are ubiquitous in the environment and are tied to myriad health effects. Despite the phasing out of the manufacturing of two types of PFASs (perfluorosulfonic acid (PFOS) and perfluorooctanoic acid (PFOA)), chemical composition renders them effectively indestructible by ambient environmental processes, where they thus remain in water. Exposure via water can affect both human and aquatic wildlife. PFASs easily cross the placenta, exposing the fetus at critical windows of development. Little is known about the effects of low-level exposure during this period; even less is known about the potential for multi- and transgenerational effects. We examined the effects of ultra-low, very low, and low-level PFAS exposure (7, 70, and 700 ng/L PFOA; 24, 240, 2400 ng/L PFOS; and stepwise mixtures) from 0–5 days post-fertilization (dpf) on larval zebrafish (Danio rerio) mortality, morphology, behavior and gene expression and fecundity in adult F0 and F1 fish. As expected, environmentally relevant PFAS levels did not affect survival. Morphological abnormalities were not observed until the F1 and F2 generations. Behavior was affected differentially by each chemical and generation. Gene expression was increasingly perturbed in each generation but consistently showed lipid pathway disruption across all generations. Dysregulation of behavior and gene expression is heritable, even in larvae with no direct or indirect exposure. This is the first report of the transgenerational effects of PFOA, PFOS, and their mixture in terms of zebrafish behavior and untargeted gene expression.
Improving the Annotation of the Venom Gland Transcriptome of Pamphobeteus verdolaga, Prospecting Novel Bioactive Peptides
Authors: Salinas-Restrepo Cristian , Misas Elizabeth , Estrada-Gómez Sebastian , Quintana-Castillo Juan Carlos , Guzman Fanny , Calderón Juan C. , Giraldo Marco A. , Segura Cesar
Published: June 2022

Spider venoms constitute a trove of novel peptides with biotechnological interest. Paucity of next-generation-sequencing (NGS) data generation has led to a description of less than 1% of these peptides. Increasing evidence supports the underestimation of the assembled genes a single transcriptome assembler can predict. Here, the transcriptome of the venom gland of the spider Pamphobeteus verdolaga was re-assembled, using three free access algorithms, Trinity, SOAPdenovo-Trans, and SPAdes, to obtain a more complete annotation. Assembler’s performance was evaluated by contig number, N50, read representation on the assembly, and BUSCO’s terms retrieval against the arthropod dataset. Out of all the assembled sequences with all software, 39.26% were common between the three assemblers, and 27.88% were uniquely assembled by Trinity, while 27.65% were uniquely assembled by SPAdes. The non-redundant merging of all three assemblies’ output permitted the annotation of 9232 sequences, which was 23% more when compared to each software and 28% more when compared to the previous P. verdolaga annotation; moreover, the description of 65 novel theraphotoxins was possible. In the generation of data for non-model organisms, as well as in the search for novel peptides with biotechnological interest, it is highly recommended to employ at least two different transcriptome assemblers.
Mycotoxin DON Accumulation in Wheat Grains Caused by Fusarium Head Blight Are Significantly Subjected to Inoculation Methods
Authors: Xian Limei , Zhang Yuhui , Hu Yi , Zhu Suqin , Wen Zhuo , Hua Chen , Li Lei , Sun Zhengxi , Li Tao
Published: June 2022

The disease severity and mycotoxin DON content in grains caused by fusarium head blight (FHB) have been two prioritized economical traits in wheat. Reliable phenotyping is a prerequisite for genetically improving wheat resistances to these two traits. In this study, three inoculation methods: upper bilateral floret injection (UBFI), basal bilateral floret injection (BBFI), and basal rachis internode injection (BRII), were applied in a panel of 22 near-isogenic lines (NILs) contrasting in Fhb1 alleles. The results showed that inoculation methods had significant influence on both disease severity and mycotoxin accumulation in grains, and the relationship between them. UBFI method caused chronic FHB symptom characterized as slow progress of the pathogen downward from the inoculation site, which minimized the difference in disease severity of the NILs, but, unexpectedly, maximized the difference in DON content between them. The BBFI method usually caused an acute FHB symptom in susceptible lines characterized as premature spike death (PSD), which maximized the difference in disease severity, but minimized the difference in DON content in grains between resistant and susceptible lines. The BRII method occasionally caused acute FHB symptoms for susceptible lines and had relatively balanced characteristics of disease severity and DON content in grains. Therefore, two or more inoculation methods are recommended for precise and reliable evaluation of the overall resistance to FHB, including resistances to both disease spread within a spike and DON accumulation in grains.
Evidence-Based Framework to Manage Cyanobacteria and Cyanotoxins in Water and Sludge from Drinking Water Treatment Plants
Authors: Jalili Farhad , Moradinejad Saber , Zamyadi Arash , Dorner Sarah , Sauvé Sébastien , Prévost Michèle
Published: June 2022

Freshwater bodies and, consequently, drinking water treatment plants (DWTPs) sources are increasingly facing toxic cyanobacterial blooms. Even though conventional treatment processes including coagulation, flocculation, sedimentation, and filtration can control cyanobacteria and cell-bound cyanotoxins, these processes may encounter challenges such as inefficient removal of dissolved metabolites and cyanobacterial cell breakthrough. Furthermore, conventional treatment processes may lead to the accumulation of cyanobacteria cells and cyanotoxins in sludge. Pre-oxidation can enhance coagulation efficiency as it provides the first barrier against cyanobacteria and cyanotoxins and it decreases cell accumulation in DWTP sludge. This critical review aims to: (i) evaluate the state of the science of cyanobacteria and cyanotoxin management throughout DWTPs, as well as their associated sludge, and (ii) develop a decision framework to manage cyanobacteria and cyanotoxins in DWTPs and sludge. The review identified that lab-cultured-based pre-oxidation studies may not represent the real bloom pre-oxidation efficacy. Moreover, the application of a common exposure unit CT (residual concentration × contact time) provides a proper understanding of cyanobacteria pre-oxidation efficiency. Recently, reported challenges on cyanobacterial survival and growth in sludge alongside the cell lysis and cyanotoxin release raised health and technical concerns with regards to sludge storage and sludge supernatant recycling to the head of DWTPs. According to the review, oxidation has not been identified as a feasible option to handle cyanobacterial-laden sludge due to low cell and cyanotoxin removal efficacy. Based on the reviewed literature, a decision framework is proposed to manage cyanobacteria and cyanotoxins and their associated sludge in DWTPs.
Subcutaneous BoNT/A Injection for Intractable Pain and Disability in Complex Regional Pain Syndrome: A Case Report
Authors: Tereshko Yan , Dalla Torre Chiara , Lettieri Christian , Belgrado Enrico , Gigli Gian Luigi , Valente Mariarosaria
Published: June 2022

We treated a 51-year-old woman with refractory Complex Regional Pain Syndrome type I (CRPS-I) involving her left hand and forearm with subcutaneous injections of BoNT/A. The injections were performed every 3 months, with a total of six treatments. Each treatment was able to effectively improve pain and motor impairment; however, the duration of the effect was limited to only a few months. BoNT/A could improve patients’ quality of life with CRPS; however, extensive clinical studies are needed to determine its role in clinical practice.
Lipid Profile Is Negatively Associated with Uremic Toxins in Patients with Kidney Failure—A Tri-National Cohort
Authors: Hobson Sam , de Loor Henriette , Kublickiene Karolina , Beige Joachim , Evenepoel Pieter , Stenvinkel Peter , Ebert Thomas
Published: June 2022

Patients with kidney failure (KF) have a high incidence of cardiovascular (CV) disease, partly driven by insufficient clearance of uremic toxins. Recent investigations have questioned the accepted effects of adverse lipid profile and CV risk in uremic patients. Therefore, we related a panel of uremic toxins previously associated with CV morbidity/mortality to a full lipid profile in a large, tri-national, cross-sectional cohort. Total, high-density lipoprotein (HDL), non-HDL, low-density lipoprotein (LDL), and remnant cholesterol, as well as triglyceride, levels were associated with five uremic toxins in a cohort of 611 adult KF patients with adjustment for clinically relevant covariates and other patient-level variables. Univariate analyses revealed negative correlations of total, non-HDL, and LDL cholesterol with all investigated uremic toxins. Multivariate linear regression analyses confirmed independent, negative associations of phenylacetylglutamine with total, non-HDL, and LDL cholesterol, while indole-3 acetic acid associated with non-HDL and LDL cholesterol. Furthermore, trimethylamine-N-Oxide was independently and negatively associated with non-HDL cholesterol. Sensitivity analyses largely confirmed findings in the entire cohort. In conclusion, significant inverse associations between lipid profile and distinct uremic toxins in KF highlight the complexity of the uremic milieu, suggesting that not all uremic toxin interactions with conventional CV risk markers may be pathogenic.
A Pilot Randomized Controlled Trial of Botulinum Toxin Treatment Combined with Robot-Assisted Therapy, Mirror Therapy, or Active Control Treatment in Patients with Spasticity Following Stroke
Authors: Hung Jen-Wen , Yen Chu-Ling , Chang Ku-Chou , Chiang Wei-Chi , Chuang I-Ching , Pong Ya-Ping , Wu Wen-Chi , Wu Ching-Yi
Published: June 2022

Effects of the combined task-oriented trainings with botulinum toxin A (BoNT-A) injection on improving motor functions and reducing spasticity remains unclear. This study aims to investigate effects of 3 task-oriented trainings (robot-assisted therapy (RT), mirror therapy (MT), and active control treatment (AC)) in patients with stroke after BoNT-A injection. Thirty-seven patients with chronic spastic hemiplegic stroke were randomly assigned to receive RT, MT, or AC following BoNT-A injection over spastic upper extremity muscles. Each session of RT, MT, and AC was 75 min, 3 times weekly, for 8 weeks. Outcome measures were assessed at pretreatment, post-treatment, and 3-month follow-up, involving the Fugl-Meyer Assessment (FMA), Modified Ashworth Scale (MAS), Motor Activity Log (MAL), including amount of use (AOU) and quality of movement (QOM), and arm activity level. All 3 combined treatments improved FMA, MAS, and MAL. The AC induced a greater effect on QOM in MAL at the 3-month follow-up than RT or MT. All 3 combined trainings induced minimal effect on arm activity level. Our findings suggest that for patients with stroke who received BoNT-A injection over spastic UE muscles, the RT, MT, or AC UE training that followed was effective in improving motor functions, reducing spasticity, and enhancing daily function.
Fumonisins in African Countries
Authors: Yli-Mattila Tapani , Sundheim Leif
Published: June 2022

Maize and other cereals are the commodities most contaminated with fumonisins. The maize acreage is increasing in Africa, and the maize harvest provides important foods for humans and feeds for domestic animals throughout the continent. In North Africa, high levels of fumonisins have been reported from Algeria and Morocco, while low levels have been detected in the rather few fumonisin analyses reported from Tunisia and Egypt. The West African countries Burkina Faso, Cameroon, Ghana, and Nigeria all report high levels of fumonisin contamination of maize, while the few maize samples analysed in Togo contain low levels. In Eastern Africa, high levels of fumonisin contamination have been reported from the Democratic Republic of Congo, Ethiopia, Kenya, Tanzania, and Uganda. The samples analysed from Rwanda contained low levels of fumonisins. Analysis of maize from the Southern African countries Malawi, Namibia, South Africa, Zambia, and Zimbabwe revealed high fumonisin levels, while low levels of fumonisins were detected in the few analyses of maize from Botswana and Mozambique.
SARS-CoV-2 Infection of Unvaccinated Liver- and Kidney-Transplant Recipients: A Single-Center Experience of 103 Consecutive Cases
Authors: Hardgrave Hailey , Wells Allison , Nigh Joseph , Osborn Tamara , Klutts Garrett , Krinock Derek , Rude Mary Katherine , Bhusal Sushma , Burdine Lyle , Giorgakis Emmanouil
Published: June 2022

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was declared a pandemic in March 2020. Its reported impact on solid-organ-transplant-recipient morbidity and mortality has varied. The aim of this study was to present the effect of transplant status, patient comorbidities and immunosuppression modality on the survival of solid-organ-transplant recipients who contracted SAR-CoV-2 during the pre-vaccination era, at a single academic transplant center. Patients (n = 103) were assessed for 90-day mortality. A univariate analysis identified an age of over 60 years (HR = 10, p = 0.0034), Belatacept (HR = 6.1, p = 0.022), and Cyclosporine (HR = 6.1, p = 0.0089) as significant mortality risk factors; Tacrolimus was protective (HR = 0.23, p = 0.022). Common metabolic comorbidities (hypertension, diabetes, obesity) did not stand out as risk factors in our patient cohort. This study on the unvaccinated is expected to facilitate a paired comparison of outcomes in transplanted patients who contracted SARS-CoV-2 during the latter period of the pandemic, when broad SARS-CoV-2 vaccination and novel antibody treatments became broadly available.
Surface EMG in Subacute and Chronic Care after Traumatic Spinal Cord Injuries
Authors: Balbinot Gustavo
Published: June 2022

Background: Traumatic spinal cord injury (SCI) is a devastating condition commonly originating from motor vehicle accidents or falls. Trauma care after SCI is challenging; after decompression surgery and spine stabilization, the first step is to assess the location and severity of the traumatic lesion. For this, clinical outcome measures are used to quantify the residual sensation and volitional control of muscles below the level of injury. These clinical assessments are important for decision-making, including the prediction of the recovery potential of individuals after the SCI. In clinical care, this quantification is usually performed using sensation and motor scores, a semi-quantitative measurement, alongside the binary classification of the sacral sparing (yes/no). Objective: In this perspective article, I review the use of surface EMG (sEMG) as a quantitative outcome measurement in subacute and chronic trauma care after SCI. Methods: Here, I revisit the main findings of two comprehensive scoping reviews recently published by our team on this topic. I offer a perspective on the combined findings of these scoping reviews, which integrate the changes in sEMG with SCI and the use of sEMG in neurorehabilitation after SCI. Results: sEMG provides a complimentary assessment to quantify the residual control of muscles with great sensitivity and detail compared to the traditional clinical assessments. Our scoping reviews unveiled the ability of the sEMG assessment to detect discomplete lesions (muscles with absent motor scores but present sEMG). Moreover, sEMG is able to measure the spontaneous activity of motor units at rest, and during passive maneuvers, the evoked responses with sensory or motor stimulation, and the integrity of the spinal cord and descending tracts with motor evoked potentials. This greatly complements the diagnostics of the SCI in the subacute phase of trauma care and deepens our understanding of neurorehabilitation strategies during the chronic phase of the traumatic injury. Conclusions: sEMG offers important insights into the neurophysiological factors underlying sensorimotor impairment and recovery after SCIs. Although several qualitative or semi-quantitative outcome measures determine the level of injury and the natural recovery after SCIs, using quantitative measures such as sEMG is promising. Nonetheless, there are still several barriers limiting the use of sEMG in the clinical environment and a need to advance high-density sEMG technology.
Epidemiology of COVID-19 in Individuals under 18 Years Old in Cartagena, Colombia: An Ecological Study of the First 14 Months of the Pandemic
Authors: Loyola Steev , Cano-Pérez Eder , Torres-Pacheco Jaison , Malambo-Garcia Dacia , Gomez Ruben , Gomez-Camargo Doris
Published: June 2022

The epidemiology of the coronavirus disease (COVID-19) has been scarcely described in individuals under 18 years old, particularly during the first months of the pandemic. The study aimed to describe the COVID-19 epidemiology in the Colombian department of Bolívar from March 2020 to April 2021 among individuals under 18 years. Furthermore, we explored whether the use of data generated by a Bolívar reference laboratory captures the departmental epidemiology. Two information sources were used; the national COVID-19 surveillance system and the Bolívar COVID-19 reference laboratory. In using a population-based ecological approach and information from confirmed symptomatic cases, epidemic curves and heat maps were constructed to assess the COVID-19 dynamics and patterns by sex, age, and residence (Cartagena vs. 45 other municipalities). The COVID-19 incidence was comparable between males and females but varied by age group, being higher in children aged 10 years and older. Cartagena had a significantly higher number of cases and experienced early epidemic peaks. Our analyses suggest that information generated by the reference laboratory does not capture the COVID-19 departmental epidemiology, despite conducting population-based surveillance across Bolívar. The study provides a retrospective characterization of the COVID-19 epidemiology in an understudied population and information that may be useful for future evidence-based responses.
Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA
Authors: Adeleke Ismaila Adeyemi , Kavalappara Saritha Raman , McGregor Cecilia , Srinivasan Rajagopalbabu , Bag Sudeep
Published: June 2022

Cucurbits in Southeastern USA have experienced a drastic decline in production over the years due to the effect of economically important viruses, mainly those transmitted by the sweet potato whitefly (Bemisia tabaci Gennadius). In cucurbits, these viruses can be found as a single or mixed infection, thereby causing significant yield loss. During the spring of 2021, surveys were conducted to evaluate the incidence and distribution of viruses infecting cantaloupe (n = 80) and watermelon (n = 245) in Georgia. Symptomatic foliar tissues were collected from six counties and sRNA libraries were constructed from seven symptomatic samples. High throughput sequencing (HTS) analysis revealed the presence of three different new RNA viruses in Georgia: cucumis melo endornavirus (CmEV), cucumis melo amalgavirus (CmAV1), and cucumis melo cryptic virus (CmCV). Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed the presence of CmEV and CmAV1 in 25% and 43% of the total samples tested, respectively. CmCV was not detected using RT-PCR. Watermelon crinkle leaf-associated virus 1 (WCLaV-1), recently reported in GA, was detected in 28% of the samples tested. Furthermore, RT-PCR and PCR analysis of 43 symptomatic leaf tissues collected from the fall-grown watermelon in 2019 revealed the presence of cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and cucurbit leaf crumple virus (CuLCrV) at 73%, 2%, and 81%, respectively. This finding broadens our knowledge of the prevalence of viruses in melons in the fall and spring, as well as the geographical expansion of the WCLaV-1 in GA, USA.
SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay
Authors: Holland Steven C. , Bains Ajeet , Holland LaRinda A. , Smith Matthew F. , Sullins Regan A. , Mellor Nicholas J. , Thomas Alexis W. , Johnson Nathaniel , Murugan Vel , Lim Efrem S.
Published: June 2022

As the SARS-CoV-2 virus evolves, mutations may result in diminished sensitivity to qRT-PCR diagnostic assays. We investigated four polymorphisms circulating in the SARS-CoV-2 Delta lineage that result in N gene target failure (NGTF) on the TaqPath COVID-19 Combo Kit. These mutations were detected from the SARS-CoV-2 genome sequences that matched with the diagnostic assay results of saliva specimens. Full length N genes from the samples displaying NGTF were cloned into plasmids and assayed using three SARS-CoV-2 qRT-PCR assays. These constructs resulted in reduced sensitivity to the TaqPath COVID-19 Combo Kit compared to the controls (mean Ct differences of 3.06, 7.70, 12.46, and 14.12), but were detected equivalently on the TaqPath COVID-19 Fast PCR Combo 2.0 or CDC 2019_nCoV_N2 assays. This work highlights the importance of genomic sequencing to monitor circulating mutations and provide guidance in improving diagnostic assays.
Pathogenesis of West Nile Virus Lineage 2 in Domestic Geese after Experimental Infection
Authors: Reemtsma Hannah , Holicki Cora M. , Fast Christine , Bergmann Felicitas , Eiden Martin , Groschup Martin H. , Ziegler Ute
Published: June 2022

West Nile virus (WNV) is an emerging infectious pathogen circulating between mosquitoes and birds but also infecting mammals. WNV has become autochthonous in Germany, causing striking mortality rates in avifauna and occasional diseases in humans and horses. We therefore wanted to assess the possible role of free-ranging poultry in the WNV transmission cycle and infected 15 goslings with WNV lineage 2 (German isolate). The geese were monitored daily and sampled regularly to determine viremia, viral shedding, and antibody development by molecular and serological methods. Geese were euthanized at various time points post-infection (pi). All infected geese developed variable degrees of viremia from day 1 to day 10 (maximum) and actively shed virus from days 2 to 7 post-infection. Depending on the time of death, the WN viral genome was detected in all examined tissue samples in at least one individual by RT-qPCR and viable virus was even re-isolated, except for in the liver. Pathomorphological lesions as well as immunohistochemically detectable viral antigens were found mainly in the brain. Furthermore, all of the geese seroconverted 6 days pi at the latest. In conclusion, geese are presumably not functioning as important amplifying hosts but are suitable sentinel animals for WNV surveillance.
A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley
Authors: Dahan Jennifer , Wolf Yuri I. , Orellana Gardenia E. , Wenninger Erik J. , Koonin Eugene V. , Karasev Alexander V.
Published: June 2022

Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and RT-PCR. The two most common viruses found were alfalfa mosaic virus and bean leafroll virus, along with Medicago sativa amalgavirus, two alphapartitiviruses, and one deltapartitivirus. Additionally, a new flavi-like virus with an unusual genome organization was discovered, dubbed Snake River alfalfa virus (SRAV). The 11,745 nt, positive-sense (+) RNA genome of SRAV encodes a single 3835 aa polyprotein with only two identifiable conserved domains, an RNA-dependent RNA polymerase (RdRP) and a predicted serine protease. Notably, unlike all +RNA virus genomes in the similar size range, the SRAV polyprotein contained no predicted helicase domain. In the RdRP phylogeny, SRAV was placed inside the flavi-like lineage as a sister clade to a branch consisting of hepaci-, and pegiviruses. To the best of our knowledge, SRAV is the first flavi-like virus identified in a plant host. Although commonly detected in alfalfa crops in southern Idaho, SRAV sequences were also amplified from thrips feeding in alfalfa stands in the area, suggesting a possible role of Frankliniella occidentalis in virus transmission.
ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein
Authors: Ballmann Rico , Hotop Sven-Kevin , Bertoglio Federico , Steinke Stephan , Heine Philip Alexander , Chaudhry M. Zeeshan , Jahn Dieter , Pucker Boas , Baldanti Fausto , Piralla Antonio , Schubert Maren , Čičin-Šain Luka , Brönstrup Mark , Hust Michael , Dübel Stefan
Published: June 2022

The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.
Expression of Alphavirus Nonstructural Protein 2 (nsP2) in Mosquito Cells Inhibits Viral RNA Replication in Both a Protease Activity-Dependent and -Independent Manner
Authors: Cherkashchenko Liubov , Rausalu Kai , Basu Sanjay , Alphey Luke , Merits Andres
Published: June 2022

Alphaviruses are positive-strand RNA viruses, mostly being mosquito-transmitted. Cells infected by an alphavirus become resistant to superinfection due to a block that occurs at the level of RNA replication. Alphavirus replication proteins, called nsP1-4, are produced from nonstructural polyprotein precursors, processed by the protease activity of nsP2. Trans-replicase systems and replicon vectors were used to study effects of nsP2 of chikungunya virus and Sindbis virus on alphavirus RNA replication in mosquito cells. Co-expressed wild-type nsP2 reduced RNA replicase activity of homologous virus; this effect was reduced but typically not abolished by mutation in the protease active site of nsP2. Mutations in the replicase polyprotein that blocked its cleavage by nsP2 reduced the negative effect of nsP2 co-expression, confirming that nsP2-mediated inhibition of RNA replicase activity is largely due to nsP2-mediated processing of the nonstructural polyprotein. Co-expression of nsP2 also suppressed the activity of replicases of heterologous alphaviruses. Thus, the presence of nsP2 inhibits formation and activity of alphavirus RNA replicase in protease activity-dependent and -independent manners. This knowledge improves our understanding about mechanisms of superinfection exclusion for alphaviruses and may aid the development of anti-alphavirus approaches.
SARS-CoV-2, Placental Histopathology, Gravity of Infection and Immunopathology: Is There an Association?
Authors: Resta Leonardo , Vimercati Antonella , Cazzato Gerardo , Fanelli Margherita , Scarcella Sara Vincenza , Ingravallo Giuseppe , Colagrande Anna , Sablone Sara , Stolfa Mary , Arezzo Francesca , Lettini Teresa , Rossi Roberta
Published: June 2022

(1) Background: As the pandemic months progress, more and more evidence shows that the placenta acts as a “barrier” to SARS-CoV-2, although rare cases of vertical transmission have been described. (2) Methods: In an attempt to investigate whether the symptoms’ severity was related to different placental histological characteristics and the immune microenvironment, we subdivided 29 placentas from 29 mothers positive for SARS-CoV-2 into two groups, depending on the symptomatology (moderate/severe vs. asymptomatic/mild), performing immunohistochemical investigations for CD4 + and CD8 + T lymphocytes, as well as for CD68 + macrophage. We also evaluated the immuno-expression of the ACE2 receptor at the placental level. These two groups were compared to a control group of 28 placentas from 28 SARS-CoV-2-negative healthy mothers. (3) Results: The symptoms (likely to be related to viremia) were statistically significantly correlated (p < 0.05) with histopathological changes, such as maternal malperfusion, decidual arteriopathy, blood vessel thrombus of fetal relevance. Furthermore, the immuno-expression of ACE2 was significantly lower in SARS-CoV-2-positive groups vs. control group (p = 0.001). (4) Conclusions: There is still much to study and discover regarding the relationship between SARS-CoV-2 and histological changes in placentas and how the latter might contribute to various neonatal clinical outcomes, such as prematurity.
Evaluation of New Polyclonal Antibody Developed for Serological Diagnostics of Tomato Mosaic Virus
Authors: Mrkvová Michaela , Hančinský Richard , Grešíková Simona , Kaňuková Šarlota , Barilla Ján , Glasa Miroslav , Hauptvogel Pavol , Kraic Ján , Mihálik Daniel
Published: June 2022

Plant viruses threaten agricultural production by reducing the yield, quality, and economical benefits. Tomato mosaic virus (ToMV) from the genus Tobamovirus causes serious losses in the quantity and quality of tomato production. The management of plant protection is very difficult, mainly due to the vector-less transmission of ToMV. Resistant breeding generally has low effectiveness. The most practical approach is the use of a rapid diagnostic assay of the virus’ presence before the symptoms occur in plants, followed by the eradication of virus-infected plants. Such approaches also include serological detection methods (ELISA and Western immunoblotting), where antibodies need to be developed for an immunochemical reaction. The development and characterization of polyclonal antibodies for the detection of ToMV with appropriate parameters (sensitivity, specificity, and cross-reactivity) were the subjects of this study. A new polyclonal antibody, AB-1, was developed in immunized rabbits using the modified oligopeptides with antigenic potential (sequences are revealed) derived from the coat protein of ToMV SL-1. the developed polyclonal antibody. AB-1, showed higher sensitivity when compared with commercially available analogs. It also detected ToMV in infected pepper and eggplant plants, and detected another two tobamoviruses (TMV and PMMoV) and ToMV in soil rhizosphere samples and root residues, even two years after the cultivation of the infected tomato plant.
Extracellular Polymeric Substances: Still Promising Antivirals
Authors: Bello-Morales Raquel , Andreu Sabina , Ruiz-Carpio Vicente , Ripa Inés , López-Guerrero José Antonio
Published: June 2022

Sulfated polysaccharides and other polyanions have been promising candidates in antiviral research for decades. These substances gained attention as antivirals when they demonstrated a high inhibitory effect in vitro against human immunodeficiency virus (HIV) and other enveloped viruses. However, that initial interest was followed by wide skepticism when in vivo assays refuted the initial results. In this paper we review the use of sulfated polysaccharides, and other polyanions, in antiviral therapy, focusing on extracellular polymeric substances (EPSs). We maintain that, in spite of those early difficulties, the use of polyanions and, specifically, the use of EPSs, in antiviral therapy should be reconsidered. We base our claim in several points. First, early studies showed that the main disadvantage of sulfated polysaccharides and polyanions is their low bioavailability, but this difficulty can be overcome by the use of adequate administration strategies, such as nebulization of aerosols to gain access to respiratory airways. Second, several sulfated polysaccharides and EPSs have demonstrated to be non-toxic in animals. Finally, these macromolecules are non-specific and therefore they might be used against different variants or even different viruses.
Methodology of Purification of Inactivated Cell-Culture-Grown SARS-CoV-2 Using Size-Exclusion Chromatography
Authors: Kovpak Anastasia A. , Piniaeva Anastasia N. , Gerasimov Oleg A. , Tcelykh Irina O. , Ermakova Mayya Y. , Zyrina Anna N. , Danilov Dmitry V. , Ivin Yury Y. , Kozlovskaya Liubov I. , Ishmukhametov Aydar A.
Published: June 2022

Various types of COVID-19 vaccines, including adenovirus, mRNA, and inactivated ones, have been developed and approved for clinical use worldwide. Inactivated vaccines are produced using a proven technology that is widely used for the production of vaccines for the prevention and control of infectious diseases, including influenza and poliomyelitis. The development of inactivated whole-virion vaccines commonly includes several stages: the production of cellular and viral biomass in cell culture; inactivation of the virus; filtration and ultrafiltration; chromatographic purification of the viral antigen; and formulation with stabilizers and adjuvants. In this study, the suitability of four resins for Size-Exclusion Chromatography was investigated for the purification of a viral antigen for the human COVID-19 vaccine.
Public Health Value of a Hypothetical Pneumococcal Conjugate Vaccine (PCV) Introduction: A Case Study
Authors: Chaiyakunapruk Nathorn , Song Dayoung , Lynch Julia , Kim Jerome H. , Dilokthornsakul Piyameth , Chotpitayasunondh Tawee , Mogasale Vittal
Published: June 2022

Background: Understanding the public health value of a vaccine at an early stage of development helps in valuing and prioritizing the investment needed. Here we present the potential cost-effectiveness of an upcoming 12 valent pneumococcal conjugate vaccine (PCV 12) in the case study country, Thailand. Methods: The cost-effectiveness analysis included a hypothetical scenario of three doses (2 + 1 regimen) PCV12 introduction in the national immunization program of Thailand compared to no PCV, PCV10, and PCV13 among <6 months old from a societal perspective with a lifetime horizon and one-year cycle length. Data from Thailand, as well as assumptions supported by the literature, were used in the analysis. The price of PCV12 was assumed similar to that of PCV10 or PCV13 for GAVI’s eligible countries based on inputs from stakeholder meeting. A one-way sensitivity analysis was conducted using 0.5–1.5 times the base price of PCV12. Results were presented in incremental cost-effectiveness ratio (ICER) in terms of monetary value per quality-adjusted life-year (QALY) gained. Results: Vaccination with PCV12 among a hypothetical cohort of 100,000 Thai children is expected to avert a total of 5358 cases which includes 5 pneumococcal meningitis, 43 pneumococcal bacteremia, 5144 all-cause pneumonia, and 166 all-cause acute otitis media compared to no vaccination. The national PCV12 vaccination program is a cost-saving strategy compared to the other three strategies. The one-way sensitivity analysis showed PCV12 is a cost-saving strategy when 1.5 times the base price of PCV12 was assumed. Conclusions: Within the limitations of hypothetical assumptions and price points incorporated, the study indicates the potential public health value of PCV12 in Thailand.
A New Live Auxotrophic Vaccine Induces Cross-Protection against Klebsiella pneumoniae Infections in Mice
Authors: Moscoso Miriam , Vallejo Juan A. , Cabral Maria P. , García Patricia , Fuentes-Valverde Víctor , Gato Eva , Arca-Suárez Jorge , Aja-Macaya Pablo , Bou Germán
Published: June 2022

The development of a whole-cell vaccine from bacteria auxotrophic for D-amino acids present in the bacterial cell wall is considered a promising strategy for providing protection against bacterial infections. Here, we constructed a prototype vaccine, consisting of a glutamate racemase-deficient mutant, for preventing Klebsiella pneumoniae infections. The deletion mutant lacks the murI gene and requires exogenous addition of D-glutamate for growth. The results showed that the K. pneumoniae ΔmurI strain is attenuated and includes a favourable combination of antigens for inducing a robust immune response and conferring an adequate level of cross-protection against systemic infections caused by K. pneumoniae strains, including some hypervirulent serotypes with elevated production of capsule polysaccharide as well as multiresistant K. pneumoniae strains. The auxotroph also induced specific production of IL-17A and IFN-γ. The rapid elimination of the strain from the blood of mice without causing disease suggests a high level of safety for administration as a vaccine.
COVID-19 Vaccination and Ukrainian Refugees in Poland during Russian–Ukrainian War—Narrative Review
Authors: Malchrzak Wojciech , Babicki Mateusz , Pokorna-Kałwak Dagmara , Doniec Zbigniew , Mastalerz-Migas Agnieszka
Published: June 2022

The outbreak of the Russian–Ukrainian war contributed to the largest migration movement in the 21st century. As a result, over 3 million refugees, mainly women, children and the elderly, arrived in Poland in a short space of time. Despite the ongoing war, it is important to remember that the COVID-19 pandemic is still present in the world, and before the outbreak of the war, Ukraine was struggling with its fifth wave. Furthermore, Ukraine has one of the lowest vaccination rates in Europe, not exceeding 40%. It is, therefore, reasonable to suspect that the vast majority of migrants have not been vaccinated. This situation may pose a significant epidemiological risk. Therefore, it is necessary to implement appropriate steps to determine the vaccination status of refugees and to supplement the vaccination with both the core and booster doses. In response to these needs, the government of Poland, like many other countries, has made it possible to provide free COVID-19 vaccination to persons fleeing war. In the face of massive migration, the overriding priority should be to ensure adequate medical care for refugees, including free COVID-19 vaccinations. However, it seems that the lack of willingness to vaccinate among Ukrainians is also replicated on migration. It seems reasonable that appropriate steps should be taken to increase awareness and confidence in vaccination, which may ultimately translate into increased vaccination uptake. Analyzing previous experiences, it is advisable to consider that the first step should be to promote vaccination and remind refugees of the possibility of free COVID-19 vaccination. Additionally, refugees should be encouraged to be vaccinated during every contact with health care workers.
COVID-19 Vaccines and Autoimmune Hematologic Disorders
Authors: Mingot-Castellano María Eva , Butta Nora , Canaro Mariana , Gómez del Castillo Solano María , Sánchez-González Blanca , Jiménez-Bárcenas Reyes , Pascual-Izquierdo Cristina , Caballero-Navarro Gonzalo , Entrena Ureña Laura , José González-López Tomás ,   on behalf of the GEPTI
Published: June 2022

Worldwide vaccination against SARS-CoV-2 has allowed the detection of hematologic autoimmune complications. Adverse events (AEs) of this nature had been previously observed in association with other vaccines. The underlying mechanisms are not totally understood, although mimicry between viral and self-antigens plays a relevant role. It is important to remark that, although the incidence of these AEs is extremely low, their evolution may lead to life-threatening scenarios if treatment is not readily initiated. Hematologic autoimmune AEs have been associated with both mRNA and adenoviral vector-based SARS-CoV-2 vaccines. The main reported entities are secondary immune thrombocytopenia, immune thrombotic thrombocytopenic purpura, autoimmune hemolytic anemia, Evans syndrome, and a newly described disorder, so-called vaccine-induced immune thrombotic thrombocytopenia (VITT). The hallmark of VITT is the presence of anti-platelet factor 4 autoantibodies able to trigger platelet activation. Patients with VITT present with thrombocytopenia and may develop thrombosis in unusual locations such as cerebral beds. The management of hematologic autoimmune AEs does not differ significantly from that of these disorders in a non-vaccine context, thus addressing autoantibody production and bleeding/thromboembolic risk. This means that clinicians must be aware of their distinctive signs in order to diagnose them and initiate treatment as soon as possible.