bluuebunny/crossref_metadata_2025 huggingface dataset:
Quadratic Stabilization of Linear Uncertain Positive Discrete-Time Systems
Authors: Krokavec Dušan , Filasová Anna
Published: September 2021

The paper provides extended methods for control linear positive discrete-time systems that are subject to parameter uncertainties, reflecting structural system parameter constraints and positive system properties when solving the problem of system quadratic stability. By using an extension of the Lyapunov approach, system quadratic stability is presented to become apparent in pre-existing positivity constraints in the design of feedback control. The approach prefers constraints representation in the form of linear matrix inequalities, reflects the diagonal stabilization principle in order to apply to positive systems the idea of matrix parameter positivity, applies observer-based linear state control to assert closed-loop system quadratic stability and projects design conditions, allowing minimization of an undesirable impact on matching parameter uncertainties. The method is utilised in numerical examples to illustrate the technique when applying the above strategy.
An Auditory Saliency Pooling-Based LSTM Model for Speech Intelligibility Classification
Authors: Gallardo-Antolín Ascensión , Montero Juan M.
Published: September 2021

Speech intelligibility is a crucial element in oral communication that can be influenced by multiple elements, such as noise, channel characteristics, or speech disorders. In this paper, we address the task of speech intelligibility classification (SIC) in this last circumstance. Taking our previous works, a SIC system based on an attentional long short-term memory (LSTM) network, as a starting point, we deal with the problem of the inadequate learning of the attention weights due to training data scarcity. For overcoming this issue, the main contribution of this paper is a novel type of weighted pooling (WP) mechanism, called saliency pooling where the WP weights are not automatically learned during the training process of the network, but are obtained from an external source of information, the Kalinli’s auditory saliency model. In this way, it is intended to take advantage of the apparent symmetry between the human auditory attention mechanism and the attentional models integrated into deep learning networks. The developed systems are assessed on the UA-speech dataset that comprises speech uttered by subjects with several dysarthria levels. Results show that all the systems with saliency pooling significantly outperform a reference support vector machine (SVM)-based system and LSTM-based systems with mean pooling and attention pooling, suggesting that Kalinli’s saliency can be successfully incorporated into the LSTM architecture as an external cue for the estimation of the speech intelligibility level.
Theoretical Modeling and Analysis of Directional Spectrum Emissivity and Its Pattern for Random Rough Surfaces with a Matrix Method
Authors: Hu Jianrui , Liu Zhanqiang , Zhao Jinfu , Wang Bing , Song Qinghua
Published: September 2021

The emissivity is an important surface property parameter in many fields, including infrared temperature measurement. In this research, a symmetry theoretical model of directional spectral emissivity prediction is proposed based on Gaussian random rough surface theory. A numerical solution based on a matrix method is determined based on its symmetrical characteristics. Influences of the index of refraction n and the root mean square (RMS) roughness σrms on the directional spectrum emissivity ε are analyzed and discussed. The results indicate that surfaces with higher n and lower σrms tend to have a peak in high viewing angles. On the contrary, surfaces with lower n and higher σrms tend to have a peak in low viewing angles. Experimental verifications based on infrared (IR) temperature measurement of Inconel 718 sandblasted surfaces were carried out. This model would contribute to understand random rough surfaces and their emitting properties in fields including machining, process controlling, remote sensing, etc.
Symmetry and Aesthetics in Dentistry
Authors: Runte Christoph , Dirksen Dieter
Published: September 2021

Animal bodies in general and faces in particular show mirror symmetry with respect to the median-sagittal plane, with exceptions rarely occurring. Bilateral symmetry to the median sagittal plane of the body also evolved very early. From an evolutionary point of view, it should therefore have fundamental advantages, e.g., more effective locomotion and chewing abilities. On the other hand, the recognition of bilaterally symmetric patterns is an important module in our visual perception. In particular, the recognition of faces with different spatial orientations and their identification is strongly related to the recognition of bilateral symmetry. Maxillofacial surgery and Dentistry affect effective masticatory function and perceived symmetry of the lower third of the face. Both disciplines have the ability to eliminate or mitigate asymmetries with respect to form and function. In our review, we will demonstrate symmetric structures from single teeth to the whole face. We will further describe different approaches to quantify cranial, facial and dental asymmetries by using either landmarks or 3D surface models. Severe facial asymmetries are usually caused by malformations such as hemifacial hyperplasia, injury or other diseases such as Noma or head and neck cancer. This could be an important sociobiological reason for a correlation between asymmetry and perceived disfigurement. The aim of our review is to show how facial symmetry and attractiveness are related and in what way dental and facial structures and the symmetry of their shape and color influence aesthetic perception. We will further demonstrate how modern technology can be used to improve symmetry in facial prostheses and maxillofacial surgery.
Investigation of Eigenmode-Based Coupled Oscillator Solver Applied to Ising Spin Problems
Authors: Murakami Shintaro , Ikeda Okuto , Hirukawa Yusuke , Saiki Toshiharu
Published: September 2021

We evaluate a coupled oscillator solver by applying it to square lattice (N × N) Ising spin problems for N values up to 50. The Ising problems are converted to a classical coupled oscillator model that includes both positive (ferromagnetic-like) and negative (antiferromagnetic-like) coupling between neighboring oscillators (i.e., they are reduced to eigenmode problems). A map of the oscillation amplitudes of lower-frequency eigenmodes enables us to visualize oscillator clusters with a low frustration density (unfrustrated clusters). We found that frustration tends to localize at the boundary between unfrustrated clusters due to the symmetric and asymmetric nature of the eigenmodes. This allows us to reduce frustration simply by flipping the sign of the amplitude of oscillators around which frustrated couplings are highly localized. For problems with N = 20 to 50, the best solutions with an accuracy of 96% (with respect to the exact ground state) can be obtained by simply checking the lowest ~N/2 candidate eigenmodes.
Brain Symmetry Analysis during the Use of a BCI Based on Motor Imagery for the Control of a Lower-Limb Exoskeleton
Authors: Ferrero Laura , Ortiz Mario , Quiles Vicente , Iáñez Eduardo , Flores José A. , Azorín José M.
Published: September 2021

Brain–Computer Interfaces (BCI) are systems that allow external devices to be controlled by means of brain activity. There are different such technologies, and electroencephalography (EEG) is an example. One of the most common EEG control methods is based on detecting changes in sensorimotor rhythms (SMRs) during motor imagery (MI). The aim of this study was to assess the laterality of cortical function when performing MI of the lower limb. Brain signals from five subjects were analyzed in two conditions, during exoskeleton-assisted gait and while static. Three different EEG electrode configurations were evaluated: covering both hemispheres, covering the non-dominant hemisphere and covering the dominant hemisphere. In addition, the evolution of performance and laterality with practice was assessed. Although sightly superior results were achieved with information from all electrodes, differences between electrode configurations were not statistically significant. Regarding the evolution during the experimental sessions, the performance of the BCI generally evolved positively the higher the experience was.
Prediction of Partition Coefficients in SDS Micelles by DFT Calculations
Authors: Saranjam Leila , Fuguet Elisabet , Nedyalkova Miroslava , Simeonov Vasil , Mas Francesc , Madurga Sergio
Published: September 2021

A computational methodology using Density-Functional Theory (DFT) calculations was developed to determine the partition coefficient of a compound in a solution of Sodium Dodecyl Sulfate (SDS) micelles. Different sets of DFT calculations were used to predict the free energy of a set of 63 molecules in 15 different solvents with the purpose of identifying the solvents with similar physicochemical characteristics to the studied micelles. Experimental partition coefficients were obtained from Micellar Electrokinetic Chromatography (MEKC) measurements. The experimental partition coefficient of these molecules was compared with the predicted partition coefficient in heptane/water, cyclohexane/water, N-dodecane/water, pyridine/water, acetic acid/water, decan-1-ol/water, octanol/water, propan-2-ol/water, acetone/water, propan-1-ol/water, methanol/water, 1,2-ethane diol/water, dimethyl sulfoxide/water, formic acid/water, and diethyl sulphide/water systems. It is observed that the combination of pronan-1-ol/water solvent was the most appropriated to estimate the partition coefficient for SDS micelles. This approach allowed us to estimate the partition coefficient orders of magnitude faster than the classical molecular dynamics simulations. The DFT calculations were carried out with the well-known exchange correlation functional B3LYP and with the global hybrid functional M06-2X from the Minnesota functionals with 6-31++G ** basis set. The effect of solvation was considered by the continuum model based on density (SMD). The proposed workflow for the prediction rate of the participation coefficient unveiled the symmetric balance between the experimental data and the computational methods.
Cobalt Oxide on a Nanoporous TUD-1 Catalyst for Methylene Blue Dye Interaction DFT Studies and Degradation
Authors: Pachamuthu Muthusamy Poomalai , Baskaran Sambath , Manivannan Chandrakumar , Kishore Somasundaram Chandra , Bellucci Stefano , Boopathy Ramasamy
Published: September 2021

Fenton and Fenton-like advanced oxidation processes (AOP) have been substantially utilized in wastewater treatment for the removal of organic contaminants. The present investigation explores the catalytic activity of cobalt dispersed over nanoporous silicate material (CoO/TUD-1), TUD-1, for the Fenton-type degradation of methylene blue (MB) dye present in wastewater, with hydrogen peroxide (H2O2) as an oxidant. The catalyst, which was prepared using the hydrothermal method, was characterized using analytical and spectroscopic techniques, such as X-ray diffraction (XRD), N2 adsorption–desorption isotherms, UV-visible diffuse reflectance (DR), scanning electron microscope (SEM), transmission electron microscopy (TEM) and Fourier transform infrared (FTIR). The results indicated that the CoO/TUD-1 possessed three-dimensional structures with a high surface area and a pore diameter capable of the uniform dispersion of cobalt species. Density functional theory (DFT) simulations were performed to study the most stable tetra coordinate adsorption configuration of a single Co atom on amorphous SiO2. To understand the geometric and electronic structure of this configuration, electron density differences, Bader charge, and partial density of states were examined. The results obtained from the DFT calculations confirmed the occurrence of electron transfer from the Co atom to the amorphous SiO2. The calculated adsorption energy was found to be −1.58 eV, which indicated that the MB dye was strongly adsorbed by parallel configuration mode and degraded more easily. Further, the addition of a 0.1g/L dose of the prepared CoO /TUD degraded the MB dye effectively (~95%) within 240 min of contact. Thus, CoO/TUD-1 is a potential material for the removal of organic contaminants and the degradation of dyes in wastewater treatment.
Cyanotoxins and the Nervous System
Authors: Metcalf James S. , Tischbein Maeve , Cox Paul Alan , Stommel Elijah W.
Published: September 2021

Cyanobacteria are capable of producing a wide range of bioactive compounds with many considered to be toxins. Although there are a number of toxicological outcomes with respect to cyanobacterial exposure, this review aims to examine those which affect the central nervous system (CNS) or have neurotoxicological properties. Such exposures can be acute or chronic, and we detail issues concerning CNS entry, detection and remediation. Exposure can occur through a variety of media but, increasingly, exposure through air via inhalation may have greater significance and requires further investigation. Even though cyanobacterial toxins have traditionally been classified based on their primary mode of toxicity, increasing evidence suggests that some also possess neurotoxic properties and include known cyanotoxins and unknown compounds. Furthermore, chronic long-term exposure to these compounds is increasingly being identified as adversely affecting human health.
Naturally Occurring Fusarium Species and Mycotoxins in Oat Grains from Manitoba, Canada
Authors: Islam M. Nazrul , Tabassum Mourita , Banik Mitali , Daayf Fouad , Fernando W. G. Dilantha , Harris Linda J. , Sura Srinivas , Wang Xiben
Published: September 2021

Fusarium head blight (FHB) can lead to dramatic yield losses and mycotoxin contamination in small grain cereals in Canada. To assess the extent and severity of FHB in oat, samples collected from 168 commercial oat fields in the province of Manitoba, Canada, during 2016–2018 were analyzed for the occurrence of Fusarium head blight and associated mycotoxins. Through morphological and molecular analysis, F. poae was found to be the predominant Fusarium species affecting oat, followed by F. graminearum, F. sporotrichioides, F. avenaceum, and F. culmorum. Deoxynivalenol (DON) and nivalenol (NIV), type B trichothecenes, were the two most abundant Fusarium mycotoxins detected in oat. Beauvericin (BEA) was also frequently detected, though at lower concentrations. Close clustering of F. poae and NIV/BEA, F. graminearum and DON, and F. sporotrichioides and HT2/T2 (type A trichothecenes) was detected in the principal component analysis. Sampling location and crop rotation significantly impacted the concentrations of Fusarium mycotoxins in oat. A phylogenetic analysis of 95 F. poae strains from Manitoba was conducted using the concatenated nucleotide sequences of Tef-1α, Tri1, and Tri8 genes. The results indicated that all F. poae strains belong to a monophyletic lineage. Four subgroups of F. poae strains were identified; however, no correlations were observed between the grouping of F. poae strains and sample locations/crop rotations.
Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species
Authors: Kumar Naveen , Kaushik Rahul , Tennakoon Chandana , Uversky Vladimir N. , Mishra Anamika , Sood Richa , Srivastava Pratiksha , Tripathi Meghna , Zhang Kam Y. J. , Bhatia Sandeep
Published: September 2021

Many viruses that cause serious diseases in humans and animals, including the betacoronaviruses (beta-CoVs), such as SARS-CoV, MERS-CoV, and the recently identified SARS-CoV-2, have natural reservoirs in bats. Because these viruses rely entirely on the host cellular machinery for survival, their evolution is likely to be guided by the link between the codon usage of the virus and that of its host. As a result, specific cellular microenvironments of the diverse hosts and/or host tissues imprint peculiar molecular signatures in virus genomes. Our study is aimed at deciphering some of these signatures. Using a variety of genetic methods we demonstrated that trends in codon usage across chiroptera-hosted CoVs are collaboratively driven by geographically different host-species and temporal-spatial distribution. We not only found that chiroptera-hosted CoVs are the ancestors of SARS-CoV-2, but we also revealed that SARS-CoV-2 has the codon usage characteristics similar to those seen in CoVs infecting the Rhinolophus sp. Surprisingly, the envelope gene of beta-CoVs infecting Rhinolophus sp., including SARS-CoV-2, had extremely high CpG levels, which appears to be an evolutionarily conserved trait. The dissection of the furin cleavage site of various CoVs infecting hosts revealed host-specific preferences for arginine codons; however, arginine is encoded by a wider variety of synonymous codons in the murine CoV (MHV-A59) furin cleavage site. Our findings also highlight the latent diversity of CoVs in mammals that has yet to be fully explored.
Two Sides to Every Story: Herpes Simplex Type-1 Viral Glycoproteins gB, gD, gH/gL, gK, and Cellular Receptors Function as Key Players in Membrane Fusion
Authors: Jambunathan Nithya , Clark Carolyn , Musarrat Farhana , Chouljenko Vladimir , Rudd Jared , Kousoulas Konstantin
Published: September 2021

Herpes simplex virus type-1 (HSV-1) and type-2 (HSV-2) are prototypical alphaherpesviruses that are characterized by their unique properties to infect trigeminal and dorsal root ganglionic neurons, respectively, and establish life-long latent infections. These viruses initially infect mucosal epithelial tissues and subsequently spread to neurons. They are associated with a significant disease spectrum, including orofacial and ocular infections for HSV-1 and genital and neonatal infections for HSV-2. Viral glycoproteins within the virion envelope bind to specific cellular receptors to mediate virus entry into cells. This is achieved by the fusion of the viral envelope with the plasma membrane. Similarly, viral glycoproteins expressed on cell surfaces mediate cell-to-cell fusion and facilitate virus spread. An interactive complex of viral glycoproteins gB, gD/gH/gL, and gK and other proteins mediate these membrane fusion phenomena with glycoprotein B (gB), the principal membrane fusogen. The requirement for the virion to enter neuronal axons suggests that the heterodimeric protein complex of gK and membrane protein UL20, found only in alphaherpesviruses, constitute a critical determinant for neuronal entry. This hypothesis was substantiated by the observation that a small deletion in the amino terminus of gK prevents entry into neuronal axons while allowing entry into other cells via endocytosis. Cellular receptors and receptor-mediated signaling synergize with the viral membrane fusion machinery to facilitate virus entry and intercellular spread. Unraveling the underlying interactions among viral glycoproteins, envelope proteins, and cellular receptors will provide new innovative approaches for antiviral therapy against herpesviruses and other neurotropic viruses.
A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly
Authors: Obr Martin , Schur Florian K. M. , Dick Robert A.
Published: September 2021

The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.
Increased sHLA-G Is Associated with Improved COVID-19 Outcome and Reduced Neutrophil Adhesion
Authors: Bortolotti Daria , Gentili Valentina , Rizzo Sabrina , Schiuma Giovanna , Beltrami Silvia , Spadaro Savino , Strazzabosco Giovanni , Campo Gianluca , Carosella Edgardo , Papi Alberto , Rizzo Roberta , Contoli Marco
Published: September 2021

Human leukocyte antigen (HLA) is a group of molecules involved in inflammatory and infective responses. We evaluated blood sHLA-E and sHLA-G levels in hospitalized COVID-19 patients with respiratory failure and their relationship with clinical evolution, changes in endothelial activation biomarker profile, and neutrophil adhesion. sHLA-E, sHLA-G, and endothelial activation biomarkers were quantified by ELISA assay in plasma samples. Neutrophil adhesion to endothelium was assessed in the presence/absence of patients’ plasma samples. At admission, plasma levels of sHLA-G and sHLA-E were significantly higher in COVID-19 patients with respiratory failure compared to controls. COVID-19 clinical improvement was associated with increased sHLA-G plasma levels. In COVID-19, but not in control patients, an inverse correlation was found between serum sICAM-1 and E-selectin levels and plasma sHLA-G values. The in vitro analysis of activated endothelial cells confirmed the ability of HLA-G molecules to control sICAM-1 and sE-selectin expression via CD160 interaction and FGF2 induction and consequently neutrophil adhesion. We suggest a potential role for sHLA-G in improving COVID-19 patients’ clinical condition related to the control of neutrophil adhesion to activated endothelium.
Comparative Analysis of Novel Strains of Porcine Astrovirus Type 3 in the USA
Authors: Matias Ferreyra Franco , Harmon Karen , Bradner Laura , Burrough Eric , Derscheid Rachel , Magstadt Drew , Michael Alyona , de Almeida Marcelo , Schumacher Loni , Siepker Chris , Sitthicharoenchai Panchan , Stevenson Gregory , Arruda Bailey
Published: September 2021

Porcine astrovirus type 3 (PoAstV3) has been previously identified as a cause of polioencephalomyelitis in swine and continues to cause disease in the US swine industry. Herein, we describe the characterization of both untranslated regions, frameshifting signal, putative genome-linked virus protein (VPg) and conserved antigenic epitopes of several novel PoAstV3 genomes. Twenty complete coding sequences (CDS) were obtained from 32 diagnostic cases originating from 11 individual farms/systems sharing a nucleotide (amino acid) percent identity of 89.74–100% (94.79–100%), 91.9–100% (96.3–100%) and 90.71–100% (93.51–100%) for ORF1a, ORF1ab and ORF2, respectively. Our results indicate that the 5′UTR of PoAstV3 is highly conserved highlighting the importance of this region in translation initiation while their 3′UTR is moderately conserved among strains, presenting alternative configurations including multiple putative protein binding sites and pseudoknots. Moreover, two predicted conserved antigenic epitopes were identified matching the 3′ termini of VP27 of PoAstV3 USA strains. These epitopes may aid in the design and development of vaccine components and diagnostic assays useful to control outbreaks of PoAstV3-associated CNS disease. In conclusion, this is the first analysis predicting the structure of important regulatory motifs of neurotropic mamastroviruses, which differ from those previously described in human astroviruses.
Viruses Infecting the European Catfish (Silurus glanis)
Authors: Saleh Mona , Sellyei Boglárka , Kovács Gyula , Székely Csaba
Published: September 2021

In aquaculture, disease management and pathogen control are key for a successful fish farming industry. In past years, European catfish farming has been flourishing. However, devastating fish pathogens including limiting fish viruses are considered a big threat to further expanding of the industry. Even though mainly the ranavirus (Iridoviridea) and circovirus (Circoviridea) infections are considered well- described in European catfish, more other agents including herpes-, rhabdo or papillomaviruses are also observed in the tissues of catfish with or without any symptoms. The etiological role of these viruses has been unclear until now. Hence, there is a requisite for more detailed information about the latter and the development of preventive and therapeutic approaches to complete them. In this review, we summarize recent knowledge about viruses that affect the European catfish and describe their origin, distribution, molecular characterisation, and phylogenetic classification. We also highlight the knowledge gaps, which need more in-depth investigations in the future.
Construction of a Recombinant Porcine Epidemic Diarrhea Virus Encoding Nanoluciferase for High-Throughput Screening of Natural Antiviral Products
Authors: Li Wan , Zhang Mengjia , Zheng Huijun , Zhou Peng , Liu Zheng , Jongkaewwattana Anan , Luo Rui , He Qigai
Published: September 2021

Porcine epidemic diarrhea virus (PEDV) is the predominant cause of an acute, highly contagious enteric disease in neonatal piglets. There are currently no approved drugs against PEDV infection. Here, we report the development of a nanoluciferase (NLuc)-based high-throughput screening (HTS) platform to identify novel anti-PEDV compounds. We constructed a full-length cDNA clone for a cell-adapted PEDV strain YN150. Using reverse genetics, we replaced the open reading frame 3 (ORF3) in the viral genome with an NLuc gene to engineer a recombinant PEDV expressing NLuc (rPEDV-NLuc). rPEDV-NLuc produced similar plaque morphology and showed similar growth kinetics compared with the wild-type PEDV in vitro. Remarkably, the level of luciferase activity could be stably detected in rPEDV-NLuc-infected cells and exhibited a strong positive correlation with the viral titers. Given that NLuc expression represents a direct readout of PEDV replication, anti-PEDV compounds could be easily identified by quantifying the NLuc activity. Using this platform, we screened for the anti-PEDV compounds from a library of 803 natural products and identified 25 compounds that could significantly inhibit PEDV replication. Interestingly, 7 of the 25 identified compounds were natural antioxidants, including Betulonic acid, Ursonic acid, esculetin, lithocholic acid, nordihydroguaiaretic acid, caffeic acid phenethyl ester, and grape seed extract. As expected, all of the antioxidants could potently reduce PEDV-induced oxygen species production, which, in turn, inhibit PEDV replication in a dose-dependent manner. Collectively, our findings provide a powerful platform for the rapid screening of promising therapeutic compounds against PEDV infection.
High Prevalence of Recombinant Porcine Endogenous Retroviruses (PERV-A/Cs) in Minipigs: A Review on Origin and Presence
Authors: Denner Joachim , Schuurman Hendrik Jan
Published: September 2021

Minipigs play an important role in biomedical research and they have also been used as donor animals for preclinical xenotransplantations. Since zoonotic microorganisms including viruses can be transmitted when pig cells, tissues or organs are transplanted, virus safety is an important feature in xenotransplantation. Whereas most porcine viruses can be eliminated from pig herds by different strategies, this is not possible for porcine endogenous retroviruses (PERVs). PERVs are integrated in the genome of pigs and some of them release infectious particles able to infect human cells. Whereas PERV-A and PERV-B are present in all pigs and can infect cells from humans and other species, PERV-C is present in most, but not all pigs and infects only pig cells. Recombinant viruses between PERV-A and PERV-C have been found in some pigs; these recombinants infect human cells and are characterized by high replication rates. PERV-A/C recombinants have been found mainly in minipigs of different origin. The possible reasons of this high prevalence of PERV-A/C in minipigs, including inbreeding and higher numbers and expression of replication-competent PERV-C in these animals, are discussed in this review. Based on these data, it is highly recommended to use only pig donors in clinical xenotransplantation that are negative for PERV-C.
Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness
Authors: Lee Guinevere
Published: September 2021

HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.
Synergistic Impairment of the Neurovascular Unit by HIV-1 Infection and Methamphetamine Use: Implications for HIV-1-Associated Neurocognitive Disorders
Authors: Fattakhov Nikolai , Torices Silvia , Stangis Michael , Park Minseon , Toborek Michal
Published: September 2021

The neurovascular units (NVU) are the minimal functional units of the blood–brain barrier (BBB), composed of endothelial cells, pericytes, astrocytes, microglia, neurons, and the basement membrane. The BBB serves as an important interface for immune communication between the brain and peripheral circulation. Disruption of the NVU by the human immunodeficiency virus-1 (HIV-1) induces dysfunction of the BBB and triggers inflammatory responses, which can lead to the development of neurocognitive impairments collectively known as HIV-1-associated neurocognitive disorders (HAND). Methamphetamine (METH) use disorder is a frequent comorbidity among individuals infected with HIV-1. METH use may be associated not only with rapid HIV-1 disease progression but also with accelerated onset and increased severity of HAND. However, the molecular mechanisms of METH-induced neuronal injury and cognitive impairment in the context of HIV-1 infection are poorly understood. In this review, we summarize recent progress in the signaling pathways mediating synergistic impairment of the BBB and neuronal injury induced by METH and HIV-1, potentially accelerating the onset or severity of HAND in HIV-1-positive METH abusers. We also discuss potential therapies to limit neuroinflammation and NVU damage in HIV-1-infected METH abusers.
Potential Diagnostic and Prognostic Biomarkers for Adenovirus Respiratory Infection in Children and Young Adults
Authors: Biserni Giovanni Battista , Scarpini Sara , Dondi Arianna , Biagi Carlotta , Pierantoni Luca , Masetti Riccardo , Sureshkumar Sugitha , Rocca Alessandro , Lanari Marcello
Published: September 2021

Human Adenoviruses (HAdV) are known to be potentially associated with strong inflammatory responses and morbidity in pediatric patients. Although most of the primary infections are self-limiting, the severity of clinical presentation, the elevation of the white blood cell count and inflammatory markers often mimic a bacterial infection and lead to an inappropriate use of antibiotics. In infections caused by HAdV, rapid antigen detection kits are advisable but not employed routinely; costs and feasibility of rapid syndromic molecular diagnosis may limit its use in the in-hospital setting; lymphocyte cultures and two-sampled serology are time consuming and impractical when considering the use of antibiotics. In this review, we aim to describe the principal diagnostic tools and the immune response in HAdV infections and evaluate whether markers based on the response of the host may help early recognition of HAdV and avoid inappropriate antimicrobial prescriptions in acute airway infections.
N-2-Hydroxypropyl Trimethyl Ammonium Chloride Chitosan as Adjuvant Enhances the Immunogenicity of a VP2 Subunit Vaccine against Porcine Parvovirus Infection in Sows
Authors: Zhao Kai , Gao Yuan , Hu Gaowei , Wang Lei , Cui Shangjin , Jin Zheng
Published: September 2021

Porcine parvovirus (PPV) is the most important infectious agent causing infertility in pigs, which can be prevented by routine vaccination. Successful vaccination depends on the association with potent adjuvants that can enhance the immunogenicity of antigen and activate the immune system. Polysaccharide adjuvant has low toxicity and high safety, and they can enhance the humoral, cellular and mucosal immune responses. In the present study, we prepared the VP2 protein subunit vaccine against PPV (PPV/VP2/N-2-HACC) using water-soluble N-2-Hydroxypropyl trimethyl ammonium chloride chitosan (N-2-HACC) as the vaccine adjuvant, and the ability of the PPV/VP2/N-2-HACC to induce immune responses and protect sows from PPV infection was evaluated. In vivo immunization showed that the sows immunized with the PPV/VP2/N-2-HACC by intramuscular injection produced higher HI antibody levels and long-term immune protection compared with the other groups, while the subunit vaccine did not stimulate the proliferation of CD4+ and CD8+ T lymphocytes to trigger the secretion of higher levels of IL-2, IL-4, IFN-α, IFN-β, and IFN-γ, indicating that the PPV/VP2/N-2-HACC mainly induced humoral immunity rather than cellular immunity. PPV was not detected in the viscera of the sows immunized with the PPV/VP2/N-2-HACC, and the protective efficacy was 100%. Collectively, our findings suggested that the N-2-HACC was a potential candidate adjuvant, and the PPV/VP2/N-2-HACC had immense application value for the control of PPV.
Prospective Cohort Study of the Kinetics of Specific Antibodies to SARS-CoV-2 Infection and to Four SARS-CoV-2 Vaccines Available in Serbia, and Vaccine Effectiveness: A 3-Month Interim Report
Authors: Lijeskić Olivera , Klun Ivana , Stamenov Djaković Marija , Gligorić Nenad , Štajner Tijana , Srbljanović Jelena , Djurković-Djaković Olgica
Published: September 2021

Real-life data on the performance of vaccines against SARS-CoV-2 are still limited. We here present the rates of detection and levels of antibodies specific for the SARS-CoV-2 spike protein RBD (receptor binding domain) elicited by four vaccines available in Serbia, including BNT-162b2 (BioNTech/Pfizer), BBIBP-CorV (Sinopharm), Gam-COVID-Vac (Gamaleya Research Institute) and ChAdOx1-S (AstraZeneca), compared with those after documented COVID-19, at 6 weeks and 3 months post first vaccine dose or post-infection. Six weeks post first vaccine dose, specific IgG antibodies were detected in 100% of individuals fully vaccinated with BNT-162b2 (n = 100) and Gam-COVID-Vac (n = 12) and in 81.7% of BBIBP-CorV recipients (n = 148), while one dose of ChAdOx1-S (n = 24) induced specific antibodies in 75%. Antibody levels elicited by BNT-162b2 were higher, while those elicited by BBIBP-CorV were lower, than after SARS-CoV-2 infection. By 3 months post-vaccination, antibody levels decreased but remained ≥20-fold above the cut-off in BNT-162b2 but not in BBIBP-CorV recipients, when an additional 30% were seronegative. For all vaccines, antibody levels were higher in individuals with past COVID-19 than in naïve individuals. A total of twelve new infections occurred within the first 3 months post-vaccination, eight after the first dose of BNT-162b2 and ChAdOx1-S (one each) and BBIBP-CorV (six), and four after full vaccination with BBIBP-CorV, but none required hospitalization.
Oral Peptide Vaccine against Hookworm Infection: Correlation of Antibody Titers with Protective Efficacy
Authors: Shalash Ahmed O. , Becker Luke , Yang Jieru , Giacomin Paul , Pearson Mark , Hussein Waleed M. , Loukas Alex , Skwarczynski Mariusz , Toth Istvan
Published: September 2021

Approximately 0.4 billion individuals worldwide are infected with hookworm. An effective vaccine is needed to not only improve the health of those affected and at high risk, but also to improve economic growth in disease-endemic areas. An ideal anti-hookworm therapeutic strategy for mass administration is a stable and orally administered vaccine. Oral vaccines are advantageous as they negate the need for trained medical staff for administration and do not require strict sterility conditions. Vaccination, therefore, can be carried out at a significantly reduced cost. One of the most promising current antigenic targets for hookworm vaccine development is the aspartic protease digestive enzyme (APR-1). Antibody-mediated neutralization of APR-1 deprives the worm of nourishment, leading to reduced worm burdens in vaccinated hosts. Previously, we demonstrated that, when incorporated into vaccine delivery systems, the APR-1-derived p3 epitope (TSLIAGPKAQVEAIQKYIGAEL) was able to greatly reduce worm burdens (≥90%) in BALB/c mice; however, multiple, large doses of the vaccine were required. Here, we investigated a variety of p3-antigen conjugates to optimize antigen delivery and establish immune response/protective efficacy relationships. We synthesized, purified, and characterized four p3 peptide-based vaccine candidates with: (a) lipidic (lipid core peptide (LCP)); (b) classical polymeric (polymethylacrylate (PMA)); and (c) novel polymeric (polyleucine in a branched or linear arrangement, BL10 or LL10, respectively) groups as self-adjuvanting moieties. BL10 and LL10 induced the highest serum anti-p3 and anti-APR-1 IgG titers. Upon challenge with rodent hookworms, the highest significant reduction in worm burden was observed in mice immunized with LL10. APR-1-specific serum IgG titers correlated with worm burden reduction. Thus, we provide the first vaccine-triggered immune response-protection relationship for hookworm infection.
Intent to Vaccinate SARS-CoV-2 Infected Children in US Households: A Survey
Authors: Teherani Mehgan , Banskota Samridhi , Camacho-Gonzalez Andres , Smith Alison G. C. , Anderson Evan J. , Kao Carol M. , Crepy D’Orleans Charles , Shane Andi L. , Lu Austin , Jaggi Preeti
Published: September 2021

A paucity of data exists evaluating a guardian’s intent to vaccinate their child against COVID-19 in the United States. We administered 102 first (April–November 2020) and 45 second (December–January 2020–2021) surveys to guardians of children (<18 years) who had a laboratory-confirmed diagnosis of COVID-19 and assessed their intent to give a COVID-19 vaccine to their child, when one becomes available. The first and second surveys of the same cohort of guardians were conducted before and following the press releases detailing the adult Pfizer-BioNTech and Moderna Phase 3 results. Both surveys included an intent-to-vaccinate question using the subjective language of “if a safe and effective vaccine” became available, and a second question was added to second surveys using the objective language of “would prevent 19 of 20 people from getting disease”. When using subjective language, 24 of 45 (53%) guardians endorsed vaccine administration for their children in the first survey, which decreased to 21 (46%) in the second survey. When adding objective language, acceptance of vaccination increased to 31 (69%, p = 0.03). Common reasons for declining vaccination were concerns about adverse effects and/or vaccine safety. Providing additional facts on vaccine efficacy increased vaccine acceptance. Evidence-based strategies are needed to increase pediatric COVID-19 vaccine uptake.
Nucleotide Pool Imbalance and Antibody Gene Diversification
Authors: Azhar Asim , Begum Nasim A. , Husain Afzal
Published: September 2021

The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
Carbamazepine Levels Related to the Demographic Indicators in Groundwater of Densely Populated Area
Authors: Ebrahimzadeh Salma , Castiglioni Sara , Riva Francesco , Zuccato Ettore , Azzellino Arianna
Published: September 2021

Consumption of pharmaceuticals by people is growing. Carbamazepine (CBZ) is an extensively used anti-epileptic drug that is recalcitrant to degradation. As a result, CBZ has been widely detected in the aquatic ecosystem due to its daily consumption and drainage in sewage systems. Leakages from sewage networks and septic tanks may represent one of the main sources of CBZ in groundwater. In this study, CBZ concentrations in groundwater and their correlations with the demographic structure of the population were investigated in the densely populated Milan urban area. Seventy-six demographic variables were retrieved from the Italian Population and Housing census. Twenty-one groundwater samples were collected from unconfined and semi-confined aquifers of the Milan area and the concentration of CBZ was measured. Groundwater CBZ levels in both aquifers were associated with the demographic data within a circular buffer with a radius of 1.5 km. All data were analyzed using a multivariate statistical approach. The results showed a significant association (p < 0.05) between CBZ concentrations and specific demographic segments of the population. Higher CBZ concentrations were found to be associated with the population aged 70 years and over (aging index), and with families having children aged under 5 years (family index). In addition, the divorce index was correlated with the high concentration of CBZ, whereas the educated and sexagenarian population showed a negative correlation. Our results indicated that the contamination of CBZ follows the same pattern in unconfined and semi-confined aquifers, which are used for drinking water purposes in Milan area. Therefore, changing the CBZ consumption pattern or replacing CBZ with other drugs may strongly influence groundwater contamination of the investigated area.
The Life Cycle Environmental Performance of On-Site or Decentralised Wastewater Treatment Systems for Domestic Homes
Authors: Gallagher John , Gill Laurence W.
Published: September 2021

There is little knowledge regarding the environmental sustainability of domestic on-site or decentralised wastewater treatment systems (DWWTS). This study evaluated six unique life cycle environmental impacts for different DWTTS configurations of five conventional septic tank systems, four packaged treatment units, and a willow evapotranspiration system. Similar freshwater eutrophication (FE), dissipated water (DW), and mineral and metal (MM), burdens were noted between the packaged and conventional system configurations, with the packaged systems demonstrating significantly higher impacts of between 18% and 56% for climate change (CC), marine eutrophication (ME), and fossils (F). At a system level, higher impacts were observed in systems requiring (i) three vs. two engineered treatment stages, (ii) a larger soil percolation trench area, and (iii) pumping of effluent. The evapotranspiration system presented the smallest total environmental impacts (3.0–10.8 lower), with net benefits for FE, ME, and MM identified due to the biomass (wood) production offsetting these burdens. Further analysis highlighted the sensitivity of results to biomass yield, operational demands (desludging or pumping energy demands), and embodied materials, with less significant impacts for replacing mechanical components, i.e., pumps. The findings highlighted the variation in environmental performance of different DWTTS configurations and indicated opportunities for design improvements to reduce their life cycle impacts.
A Cloud-Based Framework for Large-Scale Monitoring of Ocean Plastics Using Multi-Spectral Satellite Imagery and Generative Adversarial Network
Authors: Jamali Ali , Mahdianpari Masoud
Published: September 2021

Marine debris is considered a threat to the inhabitants, as well as the marine environments. Accumulation of marine debris, besides climate change factors, including warming water, sea-level rise, and changes in oceans’ chemistry, are causing the potential collapse of the marine environment’s health. Due to the increase of marine debris, including plastics in coastlines, ocean and sea surfaces, and even in deep ocean layers, there is a need for developing new advanced technology for the detection of large-sized marine pollution (with sizes larger than 1 m) using state-of-the-art remote sensing and machine learning tools. Therefore, we developed a cloud-based framework for large-scale marine pollution detection with the integration of Sentinel-2 satellite imagery and advanced machine learning tools on the Sentinel Hub cloud application programming interface (API). Moreover, we evaluated the performance of two shallow machine learning algorithms of random forest (RF) and support vector machine (SVM), as well as the deep learning method of the generative adversarial network-random forest (GAN-RF) for the detection of ocean plastics in the pilot site of Mytilene Island, Greece. Based on the obtained results, the shallow algorithms of RF and SVM achieved an overall accuracy of 88% and 84%, respectively, with available training data of plastic debris. The GAN-RF classifier improved the detection of ocean plastics of the RF method by 8%, achieving an overall accuracy of 96% by generating several synthetic ocean plastic samples.
Sheet-like Skeleton Carbon Derived from Shaddock Peels with Hierarchically Porous Structures for Ultra-Fast Removal of Methylene Blue
Authors: Dong Panlong , Liu Hailin , Xu Shengrui , Chen Changpo , Feng Suling , Long Anying
Published: September 2021

To remove the pollutant methylene blue (MB) from water, a sheet-like skeleton carbon derived from shaddock peels (SPACs) was prepared by NaOH activation followed by a calcination procedure under nitrogen protection in this study. Characterization results demonstrated that the as-prepared SPACs displayed a hierarchically porous structure assembled with a thin sheet-like carbon layer, and the surface area of SPAC-8 (activated by 8 g NaOH) was up to 782.2 m2/g. The as-prepared carbon material presented an ultra-fast and efficient adsorption capacity towards MB due to its macro-mesoporous structure, high surface area, and abundant functional groups. SPAC-8 showed ultrafast and efficient removal capacity for MB dye. Adsorption equilibrium was reached within 1 min with a removal efficiency of 99.6% at an initial concentration of 100 mg/g under batch adsorption model conditions. The maximum adsorption capacity for MB was up to 432.5 mg/g. A pseudo-second-order kinetic model and a Langmuir isotherm model described the adsorption process well, which suggested that adsorption rate depended on chemisorption and the adsorption process was controlled by a monolayer adsorption, respectively. Furthermore, column adsorption experiments showed that 96.58% of MB was removed after passing through a SPAC-8 packed column with a flow rate of 20 mL/min, initial concentration of 50 mg/L, and adsorbent dosage of 5 mg. The as-prepared adsorbent displays potential value in practical applications for dye removal due to its ultrafast and efficient adsorption capacity.