bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Transient Thermal Distribution in a Convective–Radiative Moving Rod Using Two-Dimensional Differential Transform Method with Multivariate Pade Approximant
Authors: Sowmya Ganeshappa , Sarris Ioannis E. , Vishalakshi Chandra Sen , Kumar Ravikumar Shashikala Varun , Prasannakumara Ballajja Chandrappa
Published: September 2021

The transient temperature distribution through a convective-radiative moving rod with temperature-dependent internal heat generation and non-linearly varying temperature-dependent thermal conductivity is elaborated in this investigation. Symmetries are intrinsic and fundamental features of the differential equations of mathematical physics. The governing energy equation subjected to corresponding initial and boundary conditions is non-dimensionalized into a non-linear partial differential equation (PDE) with the assistance of relevant non-dimensional terms. Then the resultant non-dimensionalized PDE is solved analytically using the two-dimensional differential transform method (2D DTM) and multivariate Pade approximant. The consequential impact of non-dimensional parameters such as heat generation, radiative, temperature ratio, and conductive parameters on dimensionless transient temperature profiles has been scrutinized through graphical elucidation. Furthermore, these graphs indicate the deviations in transient thermal profile for both finite difference method (FDM) and 2D DTM-multivariate Pade approximant by considering the forced convective and nucleate boiling heat transfer mode. The results reveal that the transient temperature profile of the moving rod upsurges with the change in time, and it improves for heat generation parameter. It enriches for the rise in the magnitude of Peclet number but drops significantly for greater values of the convective-radiative and convective-conductive parameters.
Molecular Mechanism of Processive Stepping of Kinesin Motors
Authors: Xie Ping
Published: September 2021

Kinesin-1 is a motor protein that can step processively on microtubule by hydrolyzing ATP molecules, playing an essential role in intracellular transports. To better understand the mechanochemical coupling of the motor stepping cycle, numerous structural, biochemical, single molecule, theoretical modeling and numerical simulation studies have been undertaken for the kinesin-1 motor. Recently, a novel ultraresolution optical trapping method was employed to study the mechanics of the kinesin-1 motor and new results were supplemented to its stepping dynamics. In this commentary, the new single molecule results are explained well theoretically with one of the models presented in the literature for the mechanochemical coupling of the kinesin-1 motor. With the model, various prior experimental results for dynamics of different families of N-terminal kinesin motors have also been explained quantitatively.
Microbial Transglutaminase Is a Very Frequently Used Food Additive and Is a Potential Inducer of Autoimmune/Neurodegenerative Diseases
Authors: Lerner Aaron , Benzvi Carina
Published: September 2021

Microbial transglutaminase (mTG) is a heavily used food additive and its industrial transamidated complexes usage is rising rapidly. It was classified as a processing aid and was granted the GRAS (generally recognized as safe) definition, thus escaping full and thorough toxic and safety evaluations. Despite the manufacturers claims, mTG or its cross-linked compounds are immunogenic, pathogenic, proinflammatory, allergenic and toxic, and pose a risk to public health. The enzyme is a member of the transglutaminase family and imitates the posttranslational modification of gluten, by the tissue transglutaminase, which is the autoantigen of celiac disease. The deamidated and transamidated gliadin peptides lose their tolerance and induce the gluten enteropathy. Microbial transglutaminase and its complexes increase intestinal permeability, suppresses enteric protective pathways, enhances microbial growth and gliadin peptide’s epithelial uptake and can transcytose intra-enterocytically to face the sub-epithelial immune cells. The present review updates on the potentially detrimental side effects of mTG, aiming to interest the scientific community, induce food regulatory authorities’ debates on its safety, and protect the public from the mTG unwanted effects.
Formulation and Safety Tests of a Wickerhamomyces anomalus–Based Product: Potential Use of Killer Toxins of a Mosquito Symbiotic Yeast to Limit Malaria Transmission
Authors: Cappelli Alessia , Amantini Consuelo , Maggi Federica , Favia Guido , Ricci Irene
Published: September 2021

Wickerhamomyces anomalus strain WaF17.12 is a yeast with an antiplasmodial property based on the production of a killer toxin. For its symbiotic association with Anopheles mosquitoes, it has been proposed for the control of malaria. In an applied view, we evaluated the yeast formulation by freeze-drying WaF17.12. The study was carried out by comparing yeast preparations stored at room temperature for different periods, demonstrating that lyophilization is a useful method to obtain a stable product in terms of cell growth reactivation and maintenance of the killer toxin antimicrobial activity. Moreover, cytotoxic assays on human cells were performed, showing no effects on the cell viability and the proinflammatory response. The post-formulation effectiveness of the killer toxin and the safety tests indicate that WaF17.12 is a promising bioreagent able to impair the malaria parasite in vector mosquitoes.
Staphylococcus aureus Toxins: An Update on Their Pathogenic Properties and Potential Treatments
Authors: Ahmad-Mansour Nour , Loubet Paul , Pouget Cassandra , Dunyach-Remy Catherine , Sotto Albert , Lavigne Jean-Philippe , Molle Virginie
Published: September 2021

Staphylococcus aureus is a clinically important pathogen that causes a wide range of human infections, from minor skin infections to severe tissue infection and sepsis. S. aureus has a high level of antibiotic resistance and is a common cause of infections in hospitals and the community. The rising prevalence of community-acquired methicillin-resistant S. aureus (CA-MRSA), combined with the important severity of S. aureus infections in general, has resulted in the frequent use of anti-staphylococcal antibiotics, leading to increasing resistance rates. Antibiotic-resistant S. aureus continues to be a major health concern, necessitating the development of novel therapeutic strategies. S. aureus uses a wide range of virulence factors, such as toxins, to develop an infection in the host. Recently, anti-virulence treatments that directly or indirectly neutralize S. aureus toxins have showed promise. In this review, we provide an update on toxin pathogenic characteristics, as well as anti-toxin therapeutical strategies.
Natural Occurrence of Alternaria Fungi and Associated Mycotoxins in Small-Grain Cereals from The Urals and West Siberia Regions of Russia
Authors: Orina Aleksandra S. , Gavrilova Olga P. , Gogina Nadezhda N. , Gannibal Philipp B. , Gagkaeva Tatiana Yu.
Published: September 2021

Alternaria fungi dominate the grain microbiota in many regions of the world; therefore, the detection of species that are able to produce mycotoxins has received much attention. A total of 178 grain samples of wheat, barley and oat obtained from the Urals and West Siberia regions of Russia in 2017–2019 were included in the study. Grain contamination with Alternaria fungi belonging to sections Alternaria and Infectoriae was analysed using qPCR with specific primers. The occurrence of four mycotoxins produced by Alternaria, AOH, AME, TEN, and TeA, was defined by HPLC-MS/MS. Alternaria DNA was found in all analysed grain samples. The prevalence of DNA of Alternaria sect. Alternaria fungi (range 53 × 10−4–21,731 × 10−4 pg/ng) over the DNA of Alternaria sect. Infectoriae (range 11 × 10−4‒4237 × 10−4 pg/ng) in the grain samples was revealed. Sixty-two percent of grain samples were contaminated by at least two Alternaria mycotoxins. The combination of TEN and TeA was found most often. Eight percent of grain samples were contaminated by all four mycotoxins, and only 3% of samples were free from the analysed secondary toxic metabolites. The amounts varied in a range of 2–53 µg/kg for AOH, 3–56 µg/kg for AME, 3–131 µg/kg for TEN and 9–15,000 µg/kg for TeA. To our knowledge, a new global maximum level of natural contamination of wheat grain with TeA was detected. A positive correlation between the amount of DNA from Alternaria sect. Alternaria and TeA was observed. The significant effects of cereal species and geographic origin of samples on the amounts of DNA and mycotoxins of Alternaria spp. in grain were revealed. Barley was the most heavily contaminated with fungi belonging to both sections. The content of AOH in oat grain was, on average, higher than that found in wheat and barley. The content of TEN in the grain of barley was lower than that in wheat and similar to that in oat. The content of TeA did not depend on the cereal crop. The effect of weather conditions (summer temperature and rainfall) on the final fungal and mycotoxin contamination of grain was discussed. The frequent co-occurrence of different Alternaria fungi and their mycotoxins in grain indicates the need for further studies investigating this issue.
Emergence of New ST301 Shiga Toxin-Producing Escherichia coli Clones Harboring Extra-Intestinal Virulence Traits in Europe
Authors: Cointe Aurélie , Bizot Etienne , Delannoy Sabine , Fach Patrick , Bidet Philippe , Birgy André , Weill François-Xavier , Lefèvre Sophie , Mariani-Kurkdjian Patricia , Bonacorsi Stéphane
Published: September 2021

O80:H2 enterohemorrhagic Escherichia coli (EHEC) of sequence type ST301 is one of the main serotypes causing European hemolytic and uremic syndrome, but also invasive infections, due to extra-intestinal virulence factors (VFs). Here, we determined whether other such heteropathotypes exist among ST301. EnteroBase was screened for ST301 strains that were included in a general SNP-phylogeny. French strains belonging to a new heteropathotype clone were sequenced. ST, hierarchical clusters (HC), serotype, resistome, and virulome were determined using EnteroBase, the CGE website, and local BLAST. The ST301 general phylogeny shows two groups. Group A (n = 25) is mainly composed of enteropathogenic E. coli, whereas group B (n = 55) includes mostly EHEC. Three serotypes, O186:H2, O45:H2 and O55:H9, share the same virulome as one of the O80:H2 sub-clones from which they derive subsequent O-antigen switches. The O55:H9 clone, mainly present in France (n = 29), as well as in the UK (n = 5) and Germany (n = 1), has a low background of genetic diversity (four HC20), although it has three Stx subtypes, an H-antigen switch, and genes encoding the major extra-intestinal VF yersiniabactin, and extended-spectrum beta-lactamases. Diverse heteropathotype clones genetically close to the O80:H2 clone are present among the ST301, requiring close European monitoring, especially the virulent O55:H9 clone.
Protein-Bound Uremic Toxins Lowering Effect of Sevelamer in Pre-Dialysis Chronic Kidney Disease Patients with Hyperphosphatemia: A Randomized Controlled Trial
Authors: Takkavatakarn Kullaya , Puapatanakul Pongpratch , Phannajit Jeerath , Sukkumme Warumphon , Chariyavilaskul Pajaree , Sitticharoenchai Patita , Leelahavanichkul Asada , Katavetin Pisut , Praditpornsilpa Kearkiat , Eiam-Ong Somchai , Susantitaphong Paweena
Published: September 2021

P-cresyl sulfate and indoxyl sulfate are strongly associated with cardiovascular events and all-cause mortality in chronic kidney disease (CKD). This randomized controlled trial was conducted to compare the effects between sevelamer and calcium carbonate on protein-bound uremic toxins in pre-dialysis CKD patients with hyperphosphatemia. Forty pre-dialysis CKD patients with persistent hyperphosphatemia were randomly assigned to receive either 2400 mg of sevelamer daily or 1500 mg of calcium carbonate daily for 24 weeks. A significant decrease of total serum p-cresyl sulfate was observed in sevelamer therapy compared to calcium carbonate therapy (mean difference between two groups −5.61 mg/L; 95% CI −11.01 to −0.27 mg/L; p = 0.04). There was no significant difference in serum indoxyl sulfate levels (p = 0.36). Sevelamer had effects in terms of lowering fibroblast growth factor 23 (p = 0.01) and low-density lipoprotein cholesterol levels (p = 0.04). Sevelamer showed benefits in terms of retarding CKD progression. Changes in vascular stiffness were not found in this study.
Usefulness of T-Tube in Liver Transplantation: Still Effective or Outmoded Strategy?
Authors: Incarbone Niccolò , De Carlis Riccardo , Centonze Leonardo , Palmieri Livia , Cordaro Giuseppe , Ficarelli Alberto , Vella Ivan , Buscemi Vincenzo , Lauterio Andrea , De Carlis Luciano
Published: September 2021

Introduction: T-tube placement during liver transplantation (LT) is still debated. We performed a retrospective study to evaluate the usefulness of T-tube after LT in two cohorts differing in post-transplant risk. Methods: A total of 327 LTs performed between 2015 and 2018 were included in the analysis. LTs from donation after circulatory death and living donation, split-liver transplants, and LTs with hepaticojejunostomy were excluded. T-tube was reserved for marginal grafts, high-risk recipients, and bile duct size discrepancy. A balance of risk (BAR) score of ≤9 defined the low-risk cohort (232 patients, 68 with and 164 without T-tube), while a BAR score of >9 defined the high-risk cohort (95 patients, 43 with and 52 without T-tube). Postoperative complications were estimated with the comprehensive complication index (CCI). Postoperative biliary complications were classified in anastomotic stricture (AS), non-anastomotic stricture (NAS), and biliary leakage (BL). Results: In the low-risk cohort, LTs with and without T-tube had similar rates of NAS (0 vs. 2.9%, p = 0.36), AS (2.9 vs. 2.4%, p = 0.83), and BL (1.4 vs. 2.4%, p = 0.64). Analogous outcomes were found in the high-risk cohort: NAS (0 vs. 0), AS (0 vs. 5.7%, p = 0.11), and BL (0 vs. 1.3%, p = 0.27). There were more postoperative complications among patients with T-tube, in both the low-risk (CCI 29 vs. 21, p < 0.001) and high-risk (CCI 51 vs. 29, p < 0.001) cohort. No differences in primary non-function, hepatic artery thrombosis, and mortality were observed. Conclusions: T-tube placement did not influence postoperative biliary complications. Although the two cohorts were normalized for post-transplant risk, LT recipients with T-tube had a more complicated course.
Are Trauma Surgery Simulation Courses Beneficial in Low- and Middle-Income Countries—A Systematic Review and Meta-Analysis
Authors: Hashmi Yousuf , Ayyaz Nashmeeya , Umar Hamza , Jawaid Anam , Ahmed Zubair
Published: September 2021

Despite trauma-related injuries being a leading cause of death worldwide, low- and middle-income countries (LMICs) lack the infrastructure and resources required to offer immediate surgical care, further perpetuating the risk of morbidity and mortality. In high-income countries, trauma surgery simulation courses are routinely delivered to surgeons, teaching the fundamental skills of operative trauma. This study aimed to assess whether similar courses are beneficial in LMICs and how they can be improved. We performed a systematic review and meta-analysis using MEDLINE, Embase and Google Scholar, analysing studies evaluating trauma surgery simulation in LMICs. The outcomes measured included clinical knowledge improvement, participant confidence and general course-feedback. The review was carried out in-line with PRISMA guidelines. Five studies were included, summating a population of 172 participants. In three studies, meta-analysis showed an overall significant weighted mean improvement of knowledge post-course by 22.91% (95%CI 19.53, 26.29; p < 0.00001; I2 = 0%). One study reported a significant increase in participant confidence for 20/22 of operative skills taught (p < 0.04). We conclude that these courses are beneficial in LMICs; however, further research is necessary to establish the optimum course design, and whether patient outcomes are improved following their implementation. Collaboration between international trauma institutions is essential for closing the educational resource inequality gap between higher- and lower-income countries.
Axion–Sterile Neutrino Dark Matter
Authors: Salvio Alberto , Scollo Simone
Published: September 2021

Extending the standard model with three right-handed neutrinos and a simple QCD axion sector can account for neutrino oscillations, dark matter and baryon asymmetry; at the same time, it solves the strong CP problem, stabilizes the electroweak vacuum and can implement critical Higgs inflation (satisfying all current observational bounds). We perform here a general analysis of dark matter (DM) in such a model, which we call the aνMSM. Although critical Higgs inflation features a (quasi) inflection point of the inflaton potential, we show that DM cannot receive a contribution from primordial black holes in the aνMSM. This leads to a multicomponent axion–sterile neutrino DM and allows us to relate the axion parameters, such as the axion decay constant, to the neutrino parameters. We include several DM production mechanisms: the axion production via misalignment and decay of topological defects as well as the sterile neutrino production through the resonant and non-resonant mechanisms and in the recently proposed CPT-symmetric universe.
Fundamental Tone and Overtones of Quasinormal Modes in Ringdown Gravitational Waves: A Detailed Study in Black Hole Perturbation
Authors: Sago Norichika , Isoyama Soichiro , Nakano Hiroyuki
Published: September 2021

Ringdown gravitational waves of compact object binaries observed by ground-based gravitational-wave detectors encapsulate rich information to understand remnant objects after the merger and to test general relativity in the strong field. In this work, we investigate the ringdown gravitational waves in detail to better understand their property, assuming that the remnant objects are black holes. For this purpose, we perform numerical simulations of post-merger phase of binary black holes by using the black hole perturbation scheme with the initial data given under the close-limit approximation, and we generate data of ringdown gravitational waves with smaller numerical errors than that associated with currently available numerical relativity simulations. Based on the analysis of the data, we propose an orthonormalization of the quasinormal mode functions describing the fundamental tone and overtones to model ringdown gravitational waves. Finally, through some demonstrations of the proposed model, we briefly discuss the prospects for ringdown gravitational-wave data analysis including the overtones of quasinormal modes.
Scalar–Tensor–Vector Modified Gravity in Light of the Planck 2018 Data
Authors: Moffat John W. , Toth Viktor
Published: September 2021

The recent data release by the Planck satellite collaboration presents a renewed challenge for modified theories of gravitation. Such theories must be capable of reproducing the observed angular power spectrum of the cosmic microwave background radiation. For modified theories of gravity, an added challenge lies in the fact that standard computational tools do not readily accommodate the features of a theory with a variable gravitational coupling coefficient. An alternative is to use less accurate but more easily modifiable semianalytical approximations to reproduce at least the qualitative features of the angular power spectrum. We extend a calculation that was used previously to demonstrate compatibility between the Scalar–Tensor–Vector–Gravity (STVG) theory, also known by the acronym MOG, and data from the Wilkinson Microwave Anisotropy Probe (WMAP) to show the consistency between the theory and the newly released Planck 2018 data. We find that within the limits of this approximation, the theory accurately reproduces the features of the angular power spectrum.
Status of Anomalies and Sterile Neutrino Searches at Nuclear Reactors
Authors: Schoppmann Stefan
Published: September 2021

Two anomalies at nuclear reactors, one related to the absolute antineutrino flux, one related to the antineutrino spectral shape, have drawn special attention to the field of reactor neutrino physics during the past decade. Numerous experimental efforts have been launched to investigate the reliability of flux models and to explore whether sterile neutrino oscillations are at the base of the experimental findings. This review aims to provide an overview on the status of experimental searches at reactors for sterile neutrino oscillations and measurements of the antineutrino spectral shape in mid-2021. The individual experimental approaches and results are reviewed. Moreover, global and joint oscillation and spectral shape analyses are discussed. Many experiments allow setting of constraints on sterile oscillation parameters, but cannot yet cover the entire relevant parameter space. Others find evidence in favour of certain parameter space regions. In contrast, findings on the spectral shape appear to give an overall consistent picture across experiments and allow narrowing down of contributions of certain isotopes.
Special Issue: “Viral Replication Complexes”
Authors: Verdaguer Núria , Ferrero Diego S.
Published: September 2021

Viruses are extraordinary biological entities that can only thrive as obligate intracellular parasites, exploiting other living cellular components in order to reproduce [...]
The Cross-Talk between Thrombosis and Inflammatory Storm in Acute and Long-COVID-19: Therapeutic Targets and Clinical Cases
Authors: Acanfora Domenico , Acanfora Chiara , Ciccone Marco Matteo , Scicchitano Pietro , Bortone Alessandro Santo , Uguccioni Massimo , Casucci Gerardo
Published: September 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) commonly complicates with coagulopathy. A syndrome called Long-COVID-19 is emerging recently in COVID-19 survivors, characterized, in addition to the persistence of symptoms typical of the acute phase, by alterations in inflammatory and coagulation parameters due to endothelial damage. The related disseminated intravascular coagulation (DIC) can be associated with high death rates in COVID-19 patients. It is possible to find a prothrombotic state also in Long-COVID-19. Early administration of anticoagulants in COVID-19 was suggested in order to improve patient outcomes, although exact criteria for their application were not well-established. Low-molecular-weight heparin (LMWH) was commonly adopted for counteracting DIC and venous thromboembolism (VTE), due to its pharmacodynamics and anti-inflammatory properties. However, the efficacy of anticoagulant therapy for COVID-19-associated DIC is still a matter of debate. Thrombin and Factor Xa (FXa) are well-known components of the coagulation cascade. The FXa is known to strongly promote inflammation as the consequence of increased cytokine expression. Endothelial cells and mononuclear leucocytes release cytokines, growth factors, and adhesion molecules due to thrombin activation. On the other hand, cytokines can activate coagulation. The cross-talk between coagulation and inflammation is mediated via protease-activated receptors (PARs). These receptors might become potential targets to be considered for counteracting the clinical expressions of COVID-19. SARS-CoV-2 is effectively able to activate local and circulating coagulation factors, thus inducing the generation of disseminated coagula. LMWH may be considered as the new frontier in the treatment of COVID-19 and Long-COVID-19. Indeed, direct oral anticoagulants (DOACs) may be an alternative option for both early and later treatment of COVID-19 patients due to their ability to inhibit PARs. The aim of this report was to evaluate the role of anticoagulants—and DOACs in particular in COVID-19 and Long-COVID-19 patients. We report the case of a COVID-19 patient who, after administration of enoxaparin developed DIC secondary to virosis and positivity for platelet factor 4 (PF4) and a case of Long-COVID with high residual cardiovascular risk and persistence of blood chemistry of inflammation and procoagulative state.
Novel Ratio Soluble Fms-like Tyrosine Kinase-1/Angiotensin-II (sFlt-1/ANG-II) in Pregnant Women Is Associated with Critical Illness in COVID-19
Authors: Espino-y-Sosa Salvador , Martinez-Portilla Raigam Jafet , Torres-Torres Johnatan , Solis-Paredes Juan Mario , Estrada-Gutierrez Guadalupe , Hernandez-Pacheco Jose Antonio , Espejel-Nuñez Aurora , Mateu-Rogell Paloma , Juarez-Reyes Angeles , Lopez-Ceh Francisco Eduardo , Villafan-Bernal Jose Rafael , Rojas-Zepeda Lourdes , Guzman-Guzman Iris Paola , Poon Liona C.
Published: September 2021

Background: In healthy pregnancies, components of the Renin-Angiotensin system (RAS) are present in the placental villi and contribute to invasion, migration, and angiogenesis. At the same time, soluble fms-like tyrosine kinase 1 (sFlt-1) production is induced after binding of ANG-II to its receptor (AT-1R) in response to hypoxia. As RAS plays an essential role in the pathogenesis of COVID-19, we hypothesized that angiogenic marker (sFlt-1) and RAS components (ANG-II and ACE-2) may be related to adverse outcomes in pregnant women with COVID-19; Methods: Prospective cohort study. Primary outcome was severe pneumonia. Secondary outcomes were ICU admission, intubation, sepsis, and death. Spearman’s Rho test was used to analyze the correlation between sFlt-1 and ANG-II levels. The sFlt-1/ANG-II ratio was determined and the association with each adverse outcome was explored by logistic regression analysis and the prediction was assessed using receiver-operating-curve (ROC); Results: Among 80 pregnant women with COVID-19, the sFlt-1/ANG-II ratio was associated with an increased probability of severe pneumonia (odds ratio [OR]: 1.31; p = 0.003), ICU admission (OR: 1.05; p = 0.007); intubation (OR: 1.09; p = 0.008); sepsis (OR: 1.04; p = 0.008); and death (OR: 1.04; p = 0.018); Conclusion: sFlt-1/ANG-II ratio is a good predictor of adverse events such as pneumonia, ICU admission, intubation, sepsis, and death in pregnant women with COVID-19.
Identification, Mechanism, and Treatment of Skin Lesions in COVID-19: A Review
Authors: Fernández-Lázaro Diego , Garrosa Manuel
Published: September 2021

Coronavirus disease 2019 (COVID-19) is a multisystem disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), that primarily causes respiratory symptoms. However, an increasing number of cutaneous manifestations associated with this disease have been reported. The aim of this study is to analyze the scientific literature on cutaneous manifestations associated with SARS-CoV-2 by means of a narrative literature review until June 2021. The search was conducted in the following electronic databases: Medline (PubMed), SciELO, and Cochrane Library Plus. The most common cutaneous manifestations in patients with COVID-19 are vesicular eruptions, petechial/purpuric rashes, acral lesions, liveoid lesions, urticarial rash, and maculopapular-erythematous rash. These manifestations may be the first presenting symptoms of SARS-CoV-2 infection, as is the case with acral lesions, vesicular eruptions, and urticaria. In relation to severity, the presence of liveoid lesions may be associated with a more severe course of the disease. Treatment used for dermatological lesions includes therapy with anticoagulants, corticosteroids, and antihistamines. Knowledge of the dermatologic manifestations associated with SARS-CoV-2 contributes to the diagnosis of COVID-19 in patients with skin lesions associated with respiratory symptoms or in asymptomatic patients. In addition, understanding the dermatologic lesions associated with COVID-19 could be useful to establish a personalized care plan.
Are Humanized Mouse Models Useful for Basic Research of Hepatocarcinogenesis through Chronic Hepatitis B Virus Infection?
Authors: Tsuge Masataka
Published: September 2021

Chronic hepatitis B virus (HBV) infection is a global health problem that can lead to liver dysfunction, including liver cirrhosis and hepatocellular carcinoma (HCC). Current antiviral therapies can control viral replication in patients with chronic HBV infection; however, there is a risk of HCC development. HBV-related proteins may be produced in hepatocytes regardless of antiviral therapies and influence intracellular metabolism and signaling pathways, resulting in liver carcinogenesis. To understand the mechanisms of liver carcinogenesis, the effect of HBV infection in human hepatocytes should be analyzed. HBV infects human hepatocytes through transfer to the sodium taurocholate co-transporting polypeptide (NTCP). Although the NTCP is expressed on the hepatocyte surface in several animals, including mice, HBV infection is limited to human primates. Due to this species-specific liver tropism, suitable animal models for analyzing HBV replication and developing antivirals have been lacking since the discovery of the virus. Recently, a humanized mouse model carrying human hepatocytes in the liver was developed based on several immunodeficient mice; this is useful for analyzing the HBV life cycle, antiviral effects of existing/novel antivirals, and intracellular signaling pathways under HBV infection. Herein, the usefulness of human hepatocyte chimeric mouse models in the analysis of HBV-associated hepatocarcinogenesis is discussed.
Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission
Authors: Swan David A. , Goyal Ashish , Bracis Chloe , Moore Mia , Krantz Elizabeth , Brown Elizabeth , Cardozo-Ojeda Fabian , Reeves Daniel B. , Gao Fei , Gilbert Peter B. , Corey Lawrence , Cohen Myron S. , Janes Holly , Dimitrov Dobromir , Schiffer Joshua T.
Published: September 2021

SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VEDIS), the ability to block symptomatic COVID-19. They only partially discriminate whether VEDIS is mediated by preventing infection completely, which is defined as detection of virus in the airways (VESUSC), or by preventing symptoms despite infection (VESYMP). Vaccine efficacy against transmissibility given infection (VEINF), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VEDIS > 90% in clinical trials, mediate VEDIS by VESUSC, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VEDIS is explained by VESYMP, then high VEINF would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VESUSC or both high VESYMP and high VEINF against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VEINF, which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.
Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic Oomycete Globisporangium ultimum
Authors: Fukunishi Miki , Sasai Shinsaku , Tojo Motoaki , Mochizuki Tomofumi
Published: September 2021

To further classify the oomycete viruses that have been discovered in recent years, we investigated virus infection in the plant-parasitic oomycete Globisporangium ultimum in Japan. Double-stranded RNA detection, high-throughput sequencing, and RT-PCR revealed that the G. ultimum isolate UOP226 contained two viruses related to fusarivirus and totivirus, named Pythium ultimum RNA virus 1 (PuRV1) and Pythium ultimum RNA virus 2 (PuRV2), respectively. Phylogenetic analysis of the deduced amino acid sequence of the RNA-dependent RNA polymerase (RdRp) showed that fusari-like PuRV1 belonged to a different phylogenetic group than Plasmopara viticola lesion-associated fusari virus (PvlaFV) 1–3 from oomycete Plasmopara viticola. Codon usage bias of the PuRV1 RdRp gene was more similar to those of fungi than Globisporangium and Phytophthora, suggesting that the PuRV1 ancestor horizontally transmitted to G. ultimum ancestor from fungi. Phylogenetic analysis of the deduced amino acid sequence of the RdRp of toti-like PuRV2 showed a monophyletic group with the other toti-like oomycete viruses from Globisporangium, Phytophthora, and Pl. viticola. However, the nucleotide sequences of toti-like oomycete viruses were not so homologous, suggesting the possibility of convergent evolution of toti-like oomycete viruses.
Roles of Virion-Incorporated CD162 (PSGL-1), CD43, and CD44 in HIV-1 Infection of T Cells
Authors: Murakami Tomoyuki , Ono Akira
Published: September 2021

Nascent HIV-1 particles incorporate the viral envelope glycoprotein and multiple host transmembrane proteins during assembly at the plasma membrane. At least some of these host transmembrane proteins on the surface of virions are reported as pro-viral factors that enhance virus attachment to target cells or facilitate trans-infection of CD4+ T cells via interactions with non-T cells. In addition to the pro-viral factors, anti-viral transmembrane proteins are incorporated into progeny virions. These virion-incorporated transmembrane proteins inhibit HIV-1 entry at the point of attachment and fusion. In infected polarized CD4+ T cells, HIV-1 Gag localizes to a rear-end protrusion known as the uropod. Regardless of cell polarization, Gag colocalizes with and promotes the virion incorporation of a subset of uropod-directed host transmembrane proteins, including CD162, CD43, and CD44. Until recently, the functions of these virion-incorporated proteins had not been clear. Here, we review the recent findings about the roles played by virion-incorporated CD162, CD43, and CD44 in HIV-1 spread to CD4+ T cells.
The Development of Novel Primer Sets to Specifically Amplify Each of the Five Different Deltapapillomaviruses That Cause Neoplasia after Cross-Species Infection
Authors: Munday John S. , Gedye Kristene , Daudt Cíntia , Chaves Da Silva Flavio
Published: September 2021

Bovine papillomavirus (BPV) types 1 and 2 are recognized as the main cause of equine sarcoids. However, some studies report that up to a quarter of these tumors do not contain detectible BPV1 or BPV2 DNA. The absence of detectible BPV1 or BPV2 in these sarcoids suggests the possible involvement of other papillomavirus types. Currently, five deltapapillomaviruses are recognized to cause mesenchymal neoplasia after cross-species infection. In addition to BPV1 and BPV2, BPV13 has been associated with equine sarcoids in Brazil, BPV14 has been associated with feline sarcoids, and Ovis aries papillomavirus 2 caused a sarcoid-like lesion in a pig. To investigate the cause of equine sarcoids, PCR primers were developed to specifically amplify each of the five different deltapapillomaviruses that have been associated with mesenchymal neoplasia. The specificity of these primers was confirmed using samples of formalin-fixed tissue known to contain each PV type. These primers allow rapid and sensitive detection of deltapapillomavirus DNA in equine sarcoids. As studies have revealed marked regional variability in the cause of equine sarcoids, these primers will be useful to determine the predominant PV type causing sarcoids in a region. Additionally, there is a single report describing mixed infections by BPV1 and BPV2 in equine sarcoids. The specific primer sets are expected to enable more sensitive detection of mixed infections in equine sarcoids. Determining the cause of equine sarcoids is important as vaccines are developed to prevent these common malignant neoplasms.
Bayesian Inversion of Soil Hydraulic Properties from Simplified Evaporation Experiments: Use of DREAM(ZS) Algorithm
Authors: Wang Xinghui , Wang Xu-sheng , Li Na , Wan Li
Published: September 2021

There is an increasing interest in identifying soil hydraulic properties from simplified evaporation experiments. However, the conventional simplified evaporation method includes a deficit due to using the linear assumption and not accounting for uncertainty in parameters. A suggested alternative method is assessing the parameter uncertainties through inverse modeling. We examined the combination of a Bayesian inverse method, namely, DREAM(ZS), and a numerical simulation model, namely, HYDRUS-1D, for parameter inversion with data in simplified evaporation experiments. The likelihood function could be conditioned only on pressure head observations (single-objective (SO)), or on both pressure head and evaporation rate observations (multi-objective (MO)), with different treatments on the top boundary condition. Three synthetic numerical experiments were generated in terms of the soil types of sand, loam and clay to verify the inverse modeling method. The MO approach performed better than the SO approach and linear assumption when the stage 1 evaporation rate was kept constant. However, the SO inversion was more robust when oscillations existed in the potential evaporation rate. Then, the SO inverse modeling was adopted to investigate two real experiments on loamy-sand soils and compared with the linear assumption. The linear assumption could be reliable for wet conditions with stage 1 evaporation but was not always useable for a relatively dry condition, such as that with stage 2 evaporation. The inverse modeling could be more successful in capturing the whole evaporation process of soils when both stage 1 and stage 2 were involved.
Effective Desalination of Acid Mine Drainage Using an Advanced Oxidation Process: Sodium Ferrate (VI) Salt
Authors: Munyengabe Alexis , Zvinowanda Caliphs , Ramontja James , Zvimba John Ngoni
Published: September 2021

The screening and treatment of acid mine drainage (AMD) using Na2FeO4 was explored. Elemental composition was performed, using an Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) for the raw and treated AMD. The AMD samples were collected from three different sampling sites:(Raw Tailing Water 1 (RTW1), Raw Tailing Water 2 (RTW2) and Raw Tailing Water 3 (RTW3)) in Pretoria, South Africa, with acidic pH ranging between 2.50 and 3.13. Total dissolved solids and the electrical conductivity of AMD samples ranged between 960 and 1000 mg L−1, 226 and 263 µS. cm−1, respectively. The final pH of treated water samples increased up to ≥9.5 after treatment with sodium ferrate (VI) (Na2FeO4). Liquid Na2FeO4 was quantitatively produced through a wet oxidation method and was fully characterized, using Fourier Transform Infra-Red (FTIR), X-ray Diffraction spectroscopy (XRD) and UV-Vis instruments. Na2FeO4 showed dual functions by removing metals and raising the pH of the treated water. Concentrations of most trace elements did not comply with WHO and DWAF guideline standards in raw AMD while after treatment with Na2FeO4, the concentrations were below guidelines for domestic and irrigation purposes.
Catalyst Recovery, Regeneration and Reuse during Large-Scale Disinfection of Water Using Photocatalysis
Authors: Bockenstedt Jonathan , Vidwans Niraj Ashutosh , Gentry Terry , Vaddiraju Sreeram
Published: September 2021

The deployment of photocatalysis for remediation of water has not yet been realized, although laboratory-scale studies have demonstrated promise. Accomplishing this requires the development of photocatalysis as a process, including studying its efficiencies in remedying water when high volumes of water are processed, and addressing the recovery, possible regeneration and reuse of the photocatalysts. To that end, this work is aimed at demonstrating the use of a custom-built mobile platform for disinfecting large quantities of water. The benchtop platform built is capable of processing 15.14 L (4 gallons) per minute of water, with possibility for further scale-up. Preliminary studies on the catalyst recovery, regeneration and reuse via gravity-assisted settling, centrifugation and air plasma treatment indicated that 77% of Aeroxide® P25 titania (TiO2) nanoparticle and 57% of porous TiO2 nanowire photocatalysts could be recovered and regenerated for further use. Overall, this study indicated that process improvements, including increasing the kinetics of the photocatalysis, and optimization of the efficacies of the catalyst recovery and regeneration processes will make it useful for water remediation on any scale. More importantly, the portable and flexible nature of the benchtop photocatalysis system makes it amenable for use in conjunction with existing technologies for remedying large quantities of water.
Applying a Graphical Method in Evaluation of Empirical Methods for Estimating Time of Concentration in an Arid Region
Authors: Zahraei Ali , Baghbani Ramin , Linhoss Anna
Published: September 2021

At gauged watersheds, the time of concentration can be estimated using rainfall-runoff data; however, at ungauged watersheds, empirical methods are used instead. Large errors in the application of empirical methods may cause inaccurate modeling of floods and unreliable structure design. In this paper, methods for calculating the time of concentration (Tc) were compared to identify the best equation for estimating Tc in ungauged watersheds of an arid region. The graphical method, based on measured data, was compared to 15 empirical methods to determine which empirical method returned the best results. The graphical method was applied to 33 rainfall-runoff events in four rural sub-watersheds located in the central parts of Hormozgan province, Iran. A ranking-based procedure was used to select the best performing empirical methods. To minimize bias and improve accuracy, the best performing empirical methods were modified by adjusting their formulas. According to the study, three empirical methods: (1) Williams, (2) Pilgrim and Mac Dermott, and (3) Arizona DOT, performed the best in the study areas. The results also showed that the modified Williams and Arizona DOT’s formulas were able to estimate the time of concentration in ungauged watersheds with an error lower than 1%.
Inclusion of Narrow Flow Paths between Buildings in Coarser Grids for Urban Flood Modeling: Virtual Surface Links
Authors: Ramsauer Sebastian , Leandro Jorge , Lin Qing
Published: September 2021

Urban flood modeling benefits from new remote sensing technologies, which provide high-resolution data and allow the consideration of small-scale urban key features. Since high-resolution data often result in large simulation runtimes, coarsening of the 2D grid via resampling techniques can be used to achieve a good balance between accuracy and computation time. However, the representation of urban features and topographical properties degrades, since small-scale features are blurred. Therefore, narrow flow paths between buildings are often not considered, building’s sizes are overestimated, and their arrangement in the grid changes. Thus, flow paths change and waterways are blocked, leading to incorrect inundations around buildings. This paper develops a method to improve the simulation results of coarser grids by adding virtual surface links (VSL) between buildings. The VSL mimic the flow paths of a high-resolution model in the areas of interest. The approach is developed for dual-drainage 1D/2D models. The approach shows a visible improvement at the localized level where the VSL are applied, in terms of under/overestimating flooding and a moderate overall improvement of the simulation results. Relatively to the model resolution of 2 m, the computational time, by applying this method, is reduced by 93.6% when using a 5 m grid and by 99% when using a 10 m grid. For a small test case, where the local effects are investigated, the error in the maximum water volume, relative to a grid size of 2 m, is reduced from 69.63% to 5.03% by using a 5 m grid and from 152.75% to 22.92% for a 10 m grid.
Research on Biological Fluidized Bed System Treatment Performance and Nitrogen Removal Process for Seafood Processing Wastewater with Different Operation Conditions
Authors: Ding Yi , You Hong , Sun Wei , Guo Zhansheng , Mei Junxue , Hou Xuguang , Liang Zhenlin , Li Zhipeng
Published: September 2021

In this study, the biological fluidized bed system was used to treat seafood processing wastewater. The sludge was collected from the secondary sedimentation tank of a municipal wastewater treatment plant and acclimated for 200 days before the experiment. The treatment efficiencies of simulated seafood processing wastewater by biological fluidized bed system with different sludge concentrations, different hydraulic retention times (HRTs) and different bio-carriers were studied. The results showed that the removal efficiency of nitrogen and phosphorus increased with the increasing sludge concentration and by extending hydraulic retention time, and the higher removal efficiency of nitrogen and phosphorus could be obtained with the higher specific surface area of the bio-carrier. The nitrogen removal process analysis showed that the nitrification and denitrification activity of sludge could be changed with different operation conditions resulting in different nitrogen removal efficiency in the biological fluidized bed system. This was mainly because the change tendency of the ammonia nitrogen oxidizing process, nitrite oxidizing process, nitrite reduction process and nitrate reduction process was different with different operation conditions in a high salinity environment. Theoretically, the difference of the inhibitory effect of a high-salt environment on different nitrification and denitrification processes could be used to realize shortcut nitrification denitrification by controlling a certain operation condition.
A Novel Hybrid Model for Developing Groundwater Potentiality Model Using High Resolution Digital Elevation Model (DEM) Derived Factors
Authors: Mallick Javed , Talukdar Swapan , Kahla Nabil Ben , Ahmed Mohd. , Alsubih Majed , Almesfer Mohammed K. , Islam Abu Reza Md. Towfiqul
Published: September 2021

The present work aims to build a unique hybrid model by combining six fuzzy operator feature selection-based techniques with logistic regression (LR) for producing groundwater potential models (GPMs) utilising high resolution DEM-derived parameters in Saudi Arabia’s Bisha area. The current work focuses exclusively on the influence of DEM-derived parameters on GPMs modelling, without considering other variables. AND, OR, GAMMA 0.75, GAMMA 0.8, GAMMA 0.85, and GAMMA 0.9 are six hybrid models based on fuzzy feature selection. The GPMs were validated by using empirical and binormal receiver operating characteristic curves (ROC). An RF-based sensitivity analysis was performed in order to examine the influence of GPM settings. Six hybrid algorithms and one unique hybrid model have predicted 1835–2149 km2 as very high and 3235–4585 km2 as high groundwater potential regions. The AND model (ROCe-AUC: 0.81; ROCb-AUC: 0.804) outperformed the other models based on ROC’s area under curve (AUC). A novel hybrid model was constructed by combining six GPMs (considering as variables) with the LR model. The AUC of ROCe and ROCb revealed that the novel hybrid model outperformed existing fuzzy-based GPMs (ROCe: 0.866; ROCb: 0.892). With DEM-derived parameters, the present work will help to improve the effectiveness of GPMs for developing sustainable groundwater management plans.