bluuebunny/crossref_metadata_2025 huggingface dataset:
The Development and Validation of a Measure to Assess COVID-19 Stress among College Students for Sustainable Education
Authors: Kumar V. Vineeth , Chatterjee Bhagyasree , Tankha Geetika
Published: September 2021

The impact of the COVID-19 pandemic on students’ personal, academic, and social life has been quite stressful. The threat to life from the virus, social isolation, and the need to shift from face-to-face learning to online mode has been challenging. Thus, the purpose of the present study was to develop and validate a self-administered tool to assess the source of COVID-19 pandemic stress among college students. The data was collected online using google forms in two phases. The data collected from 173 participants from phase one was analyzed using exploratory factor analysis (EFA). The second phase data of 216 participants were analyzed to validate the factor structure using confirmatory factor analysis (CFA). The standardized factor loadings, Composite Reliability (CR), and AVE of factors were assessed to determine the convergent validity of the scale. Similarly, discriminant validity and concurrent predictive validity were assessed through the HTMT ratio of correlations and ROC curves, respectively. A succession of Exploratory Factor Analysis yielded a five-factor solution, explaining 73.83 percent variance with 13 indices. CFA via maximum likelihood with bootstrapping indicated a good fit for the five-factor model (SRMR = 0.037, RMSEA = 0.049, CFI = 0.981). The standardized factor loadings, Composite Reliability (CR), and AVE of factors together suggest acceptable convergent validity. Further, the ROC curve results to assess stress indicated an acceptable AUC, with a magnitude of 0.79, p < 0.01, indicating concurrent predictive validity for the five-factor Student COVID-19 Stress Scale (SCSS). HTMT ratio of correlations <0.85 indicated discriminant validity for the factor structure. The CR > 0.70 for the dimensions indicated acceptable reliability. Thus, the SCSS can be an effective instrument to assess the source of pandemic stress among students so that tailor-made timely interventions can be provided to prevent long-term adverse effects.
HTLinker: A Head-to-Tail Linker for Nested Named Entity Recognition
Authors: Li Xiang , Yang Junan , Liu Hui , Hu Pengjiang
Published: September 2021

Named entity recognition (NER) aims to extract entities from unstructured text, and a nested structure often exists between entities. However, most previous studies paid more attention to flair named entity recognition while ignoring nested entities. The importance of words in the text should vary for different entity categories. In this paper, we propose a head-to-tail linker for nested NER. The proposed model exploits the extracted entity head as conditional information to locate the corresponding entity tails under different entity categories. This strategy takes part of the symmetric boundary information of the entity as a condition and effectively leverages the information from the text to improve the entity boundary recognition effectiveness. The proposed model considers the variability in the semantic correlation between tokens for different entity heads under different entity categories. To verify the effectiveness of the model, numerous experiments were implemented on three datasets: ACE2004, ACE2005, and GENIA, with F1-scores of 80.5%, 79.3%, and 76.4%, respectively. The experimental results show that our model is the most effective of all the methods used for comparison.
On Systems of Active Particles Perturbed by Symmetric Bounded Noises: A Multiscale Kinetic Approach
Authors: Flora Bruno Felice Filippo , Ciancio Armando , d’Onofrio Alberto
Published: September 2021

We consider an ensemble of active particles, i.e., of agents endowed by internal variables u(t). Namely, we assume that the nonlinear dynamics of u is perturbed by realistic bounded symmetric stochastic perturbations acting nonlinearly or linearly. In the absence of birth, death and interactions of the agents (BDIA) the system evolution is ruled by a multidimensional Hypo-Elliptical Fokker–Plank Equation (HEFPE). In presence of nonlocal BDIA, the resulting family of models is thus a Partial Integro-differential Equation with hypo-elliptical terms. In the numerical simulations we focus on a simple case where the unperturbed dynamics of the agents is of logistic type and the bounded perturbations are of the Doering–Cai–Lin noise or the Arctan bounded noise. We then find the evolution and the steady state of the HEFPE. The steady state density is, in some cases, multimodal due to noise-induced transitions. Then we assume the steady state density as the initial condition for the full system evolution. Namely we modeled the vital dynamics of the agents as logistic nonlocal, as it depends on the whole size of the population. Our simulations suggest that both the steady states density and the total population size strongly depends on the type of bounded noise. Phenomena as transitions to bimodality and to asymmetry also occur.
Idiopathic Interstitial Pneumonias and COVID-19 Pneumonia: Review of the Main Radiological Features and Differential Diagnosis
Authors: Guarnera Alessia , Santini Elena , Podda Pierfrancesco
Published: September 2021

COVID-19 pneumonia represents a challenging health emergency, due to the disproportion between the high transmissibility, morbidity, and mortality of the virus and healthcare systems possibilities. Literature has mainly focused on COVID-19 pneumonia clinical-radiological diagnosis and therapy, and on the most common differential diagnoses, while few papers investigated rare COVID-19 pneumonia differential diagnoses or the overlapping of COVID-19 pneumonia on pre-existing lung pathologies. This article presents the main radiological characteristics of COVID-19 pneumonia and Idiopathic Interstitial Pneumonias (IIPs) to identify key radiological features for a differential diagnosis among IIPs, and between IIPs and COVID-19 pneumonia. COVID-19 pneumonia differential diagnosis with IIPs is challenging, since these entities may share common radiological findings as ground glass opacities, crazy paving patterns, and consolidations. Multidisciplinary discussion is crucial to reach a final and correct diagnosis. Radiologists have a pivotal role in identifying COVID-19 pneumonia patterns, reporting possible overlapping with long-lasting lung diseases, and suggesting potential differential diagnoses. An optimal evaluation of HRTC may help in containing the disease, in promoting better treatment for patients, and in providing an efficient allocation of human and economic resources.
Kidney Failure after Liver Transplantation
Authors: Colliou Eloïse , Del Bello Arnaud , Milongo David , Muscari Fabrice , Vallet Marion , Tack Ivan , Kamar Nassim
Published: September 2021

One-third of patients with cirrhosis present kidney failure (AKI and CKD). It has multifactorial causes and a harmful effect on morbidity and mortality before and after liver transplantation. Kidney function does not improve in all patients after liver transplantation, and liver transplant recipients are at a high risk of developing chronic kidney disease. The causes of renal dysfunction can be divided into three groups: pre-operative, perioperative and post-operative factors. To date, there is no consensus on the modality to evaluate the risk of chronic kidney disease after liver transplantation, or for its prevention. In this narrative review, we describe the outcome of kidney function after liver transplantation, and the prognostic factors of chronic kidney disease in order to establish a risk categorization for each patient. Furthermore, we discuss therapeutic options to prevent kidney dysfunction in this context, and highlight the indications of combined liver–kidney transplantation.
Mass Composition of UHECRs from Xmax Distributions Recorded by the Pierre Auger and Telescope Array Observatories
Authors: Arsene Nicusor
Published: September 2021

In this paper we infer the mass composition of the ultra high energy cosmic rays (UHECRs) from measurements of Xmax distributions recorded at the Pierre Auger (2014) and Telescope Array (TA) (2016) Observatories, by fitting them with all possible combinations of Monte Carlo (MC) templates from a large set of primary species (p, He, C, N, O, Ne, Si and Fe), as predicted by EPOS-LHC, QGSJETII-04 and Sibyll 2.1 hadronic interaction models. We use the individual fractions of nuclei reconstructed from one experiment in each energy interval to build equivalent MC Xmax distributions, which we compare with the experimental Xmax distributions of the other experiment, applying different statistical tests of compatibility. The results obtained from both experiments confirm that the mass composition of the UHECRs is dominated (≳70%) by protons and He nuclei in the energy range investigated lgE(eV) = [17.8–19.3] (Auger) and lgE(eV) = [18.2–19.0] (TA). The indirect comparisons between the Xmax distributions recorded by the two experiments show that the degree of compatibility of the two datasets is good, even excellent in some high energy intervals, especially above the ankle (lgE(eV)∼18.7). However, our study reveals that, at low energies, further effort in data analysis is required in order to harmonize the results of the two experiments.
Advanced Virgo: Status of the Detector, Latest Results and Future Prospects
Authors: Bersanetti Diego , Patricelli Barbara , Piccinni Ornella Juliana , Piergiovanni Francesco , Salemi Francesco , Sequino Valeria
Published: September 2021

The Virgo detector, based at the EGO (European Gravitational Observatory) and located in Cascina (Pisa), played a significant role in the development of the gravitational-wave astronomy. From its first scientific run in 2007, the Virgo detector has constantly been upgraded over the years; since 2017, with the Advanced Virgo project, the detector reached a high sensitivity that allowed the detection of several classes of sources and to investigate new physics. This work reports the main hardware upgrades of the detector and the main astrophysical results from the latest five years; future prospects for the Virgo detector are also presented.
The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts
Authors: Tirera Sourakhata , de Thoisy Benoit , Donato Damien , Bouchier Christiane , Lacoste Vincent , Franc Alain , Lavergne Anne
Published: September 2021

Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.
Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies
Authors: Bateman Kelly S. , Kerr Rose , Stentiford Grant D. , Bean Tim P. , Hooper Chantelle , Van Eynde Benigna , Delbare Daan , Bojko Jamie , Christiaens Olivier , Taning Clauvis N. T. , Smagghe Guy , van Oers Monique M. , van Aerle Ronny
Published: September 2021

Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera.
Host Antiviral Responses against Avian Infectious Bronchitis Virus (IBV): Focus on Innate Immunity
Authors: Zhang Yun , Xu Zhichao , Cao Yongchang
Published: September 2021

Avian infectious bronchitis virus (IBV) is an important gammacoronavirus. The virus is highly contagious, can infect chickens of all ages, and causes considerable economic losses in the poultry industry worldwide. In the last few decades, numerous studies have been published regarding pathogenicity, vaccination, and host immunity-virus interaction. In particular, innate immunity serves as the first line of defense against invasive pathogens and plays an important role in the pathogenetic process of IBV infection. This review focuses on fundamental aspects of host innate immune responses after IBV infection, including identification of conserved viral structures and different components of host with antiviral activity, which could provide useful information for novel vaccine development, vaccination strategies, and intervention programs.
IgG-Complexed Adenoviruses Induce Human Plasmacytoid Dendritic Cell Activation and Apoptosis
Authors: Tran Thi Thu Phuong , Tran Tuan Hiep , Kremer Eric J.
Published: September 2021

Following repeat exposure to many human adenoviruses (HAdVs), most adults harbour long-lived B- and T-cell responses. Combined, this response typically protects us for years from re-infection by the same HAdV type. In spite of these immune responses, some HAdV types are associated with persistent infections that constitute a life-threatening risk when an individual’s T-cell response is compromised. By contrast, patients with B-cell deficiencies do not appear to be at a greater risk of HAdV disease. This dichotomy begs the question of the secondary role of anti-HAdV antibodies during host defence. In this study, we explored IgG-complexed (IC)-HAdV5 and primary human plasmacytoid dendritic cell (pDC) interactions. We found that IC-HAdV5 are efficiently internalized in pDCs, stimulate their activation through TLR9 signalling, and cause apoptosis. These data may help reconcile the enigma of robust immune response to HAdVs, while concurrently allowing persistence.
Newly Discovered Archival Data Show Coincidence of a Peak of Sexually Transmitted Diseases with the Early Epicenter of Pandemic HIV-1
Authors: Sousa João , Havik Philip , Müller Viktor , Vandamme Anne-Mieke
Published: September 2021

To which extent STDs facilitated HIV-1 adaptation to humans, sparking the pandemic, is still unknown. We searched colonial medical records from 1906–1958 for Leopoldville, Belgian Congo, which was the initial epicenter of pandemic HIV-1, compiling counts of treated STD cases in both Africans and Europeans. Almost all Europeans were being treated, while for Africans, generalized treatment started only in 1929. Treated STD counts in Europeans thus reflect STD infection rates more accurately compared to counts in Africans. In Africans, the highest recorded STD treatment incidence was in 1929–1935, declining to low levels in the 1950s. In Europeans, the recorded treatment incidences were highest during the period 1910–1920, far exceeding those in Africans. Europeans were overwhelmingly male and had frequent sexual contact with African females. Consequently, high STD incidence among Europeans must have coincided with high prevalence and incidence in the city’s African population. The data strongly suggest the worst STD period was 1910–1920 for both Africans and Europeans, which coincides with the estimated origin of pandemic HIV-1. Given the strong effect of STD coinfections on HIV transmission, these new data support our hypothesis of a causal effect of STDs on the epidemic emergence of HIV-1.
A Review of Treatment and Prevention of Coronavirus Disease 2019 among Solid Organ Transplant Recipients
Authors: Buehrle Deanna J. , Sutton Robert R. , McCann Erin L. , Lucas Aaron E.
Published: September 2021

Therapeutic management of solid organ transplant (SOT) recipients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), may challenge healthcare providers given a paucity of clinical data specific to this cohort. Herein, we summarize and review the studies that have formed the framework for current COVID-19 consensus management guidelines. Our review focuses on COVID-19 treatment options including monoclonal antibody products, antiviral agents such as remdesivir, and immunomodulatory agents such as corticosteroids, interleukin inhibitors, and kinase inhibitors. We highlight the presence or absence of clinical data of these therapeutics related to the SOT recipient with COVID-19. We also describe data surrounding COVID-19 vaccination of the SOT recipient. Understanding the extent and limitations of observational and clinical trial data for the prevention and treatment of COVID-19 specific to the SOT population is crucial for optimal management. Although minimal data exist on clinical outcomes among SOT recipients treated with varying COVID-19 therapeutics, reviewing these agents and the studies that have led to their inclusion or exclusion in clinical management of COVID-19 highlights the need for further studies of these therapeutics in SOT patients with COVID-19.
Multiple Autonomous Cell Death Suppression Strategies Ensure Cytomegalovirus Fitness
Authors: Mandal Pratyusha , Nagrani Lynsey N. , Hernandez Liliana , McCormick Anita Louise , Dillon Christopher P. , Koehler Heather S. , Roback Linda , Alnemri Emad S. , Green Douglas R. , Mocarski Edward S.
Published: September 2021

Programmed cell death pathways eliminate infected cells and regulate infection-associated inflammation during pathogen invasion. Cytomegaloviruses encode several distinct suppressors that block intrinsic apoptosis, extrinsic apoptosis, and necroptosis, pathways that impact pathogenesis of this ubiquitous herpesvirus. Here, we expanded the understanding of three cell autonomous suppression mechanisms on which murine cytomegalovirus relies: (i) M38.5-encoded viral mitochondrial inhibitor of apoptosis (vMIA), a BAX suppressor that functions in concert with M41.1-encoded viral inhibitor of BAK oligomerization (vIBO), (ii) M36-encoded viral inhibitor of caspase-8 activation (vICA), and (iii) M45-encoded viral inhibitor of RIP/RHIM activation (vIRA). Following infection of bone marrow-derived macrophages, the virus initially deflected receptor-interacting protein kinase (RIPK)3-dependent necroptosis, the most potent of the three cell death pathways. This process remained independent of caspase-8, although suppression of this apoptotic protease enhances necroptosis in most cell types. Second, the virus deflected TNF-mediated extrinsic apoptosis, a pathway dependent on autocrine TNF production by macrophages that proceeds independently of mitochondrial death machinery or RIPK3. Third, cytomegalovirus deflected BCL-2 family protein-dependent mitochondrial cell death through combined TNF-dependent and -independent signaling even in the absence of RIPK1, RIPK3, and caspase-8. Furthermore, each of these cell death pathways dictated a distinct pattern of cytokine and chemokine activation. Therefore, cytomegalovirus employs sequential, non-redundant suppression strategies to specifically modulate the timing and execution of necroptosis, extrinsic apoptosis, and intrinsic apoptosis within infected cells to orchestrate virus control and infection-dependent inflammation. Virus-encoded death suppressors together hold control over an intricate network that upends host defense and supports pathogenesis in the intact mammalian host.
The Impact of Risk-Adjusted Heparin Regimens on the Outcome of Patients with COVID-19 Infection. A Prospective Cohort Study
Authors: Di Micco Pierpaolo , Tufano Antonella , Cardillo Giuseppe , Imbalzano Egidio , Amitrano Maria , Lodigiani Corrado , Bellizzi Annamaria , Camporese Giuseppe , Cavalli Antonella , De Stefano Carmela , Russo Vincenzo , Voza Antonio , Perrella Alessandro , Prandoni Paolo
Published: September 2021

Background. According to recent guidelines, all hospitalized patients with COVID-19 should receive pharmacological prophylaxis for venous thromboembolism (VTE), unless there are specific contraindications. However, the optimal preventive strategy in terms of intensity of anticoagulation for these patients is not well established. Objectives. To investigate the impact of individualized regimens of enoxaparin on the development of VTE and on the risk of major bleeding complications during hospitalization in patients with COVID-19 infection. Methods. All consecutive patients admitted to the medical wards of six Italian hospitals between 15 September and 15 October 2020 with COVID-19 infection of moderate severity were administered enoxaparin in subcutaneous daily doses adjusted to the Padua Prediction Score stratification model: No heparin in patients scoring less than 4, 4000 IU daily in those scoring 4, 6000 IU in those scoring 5, and 8000 in those scoring six or more. Objective tests were performed in patients developing clinical symptoms of deep vein thrombosis and/or pulmonary embolism. Bleeding complications were defined according to the ISTH classification. Results. From the 154 eligible patients, enoxaparin was administered in all: 4000 IU in 73 patients, 6000 IU in 53, and 8000 IU in the remaining 28. During the course of hospitalization, 27 patients (17.5%) died. VTE developed in 14 of the 154 patients (9.1%; 95% CI, 4.6% to 13.6%), and was fatal in 1. Major bleeding complications developed in 35 patients (22.7%; 95% CI, 16.1% to 29.3%), and were fatal in 8. Conclusions. Despite the use of risk-adjusted doses of enoxaparin, the rate of VTE events was consistent with that reported in contemporary studies where fixed-dose low-molecular-weight heparin was used. The unexpectedly high risk of bleeding complications should induce caution in administering enoxaparin in doses higher than the conventional low ones.
An Absolutely Conserved Tryptophan in the Stem of the Envelope Protein E of Flaviviruses Is Essential for the Formation of Stable Particles
Authors: Medits Iris , Heinz Franz X. , Stiasny Karin
Published: September 2021

The major envelope protein E of flaviviruses contains an ectodomain that is connected to the transmembrane domain by the so-called “stem” region. In mature flavivirus particles, the stem is composed of two or three mostly amphipathic α-helices and a conserved sequence element (CS) with an undefined role in the viral life cycle. A tryptophan is the only residue within this region which is not only conserved in all vector-borne flaviviruses, but also in the group with no known vector. We investigated the importance of this residue in different stages of the viral life cycle by a mutagenesis-based approach using tick-borne encephalitis virus (TBEV). Replacing W421 by alanine or histidine strongly reduced the release of infectious virions and their thermostability, whereas fusion-related entry functions and virus maturation were still intact. Serial passaging of the mutants led to the emergence of a same-site compensatory mutation to leucine that largely restored these properties of the wildtype. The conserved tryptophan in CS (or another big hydrophobic amino acid at the same position) is thus essential for the assembly and infectivity of flaviviruses by being part of a network required for conferring stability to infectious particles.
Distribution and Pathogenicity of Two Cutthroat Trout Virus (CTV) Genotypes in Canada
Authors: Long Amy , LeBlanc Francis , Arseneau Jean-René , Gagne Nellie , Einer-Jensen Katja , Lovy Jan , Polinski Mark , Jones Simon , Garver Kyle A
Published: September 2021

The sole member of the Piscihepevirus genus (family Hepeviridae) is cutthroat trout virus (CTV) but recent metatranscriptomic studies have identified numerous fish hepevirus sequences including CTV-2. In the current study, viruses with sequences resembling both CTV and CTV-2 were isolated from salmonids in eastern and western Canada. Phylogenetic analysis of eight full genomes delineated the Canadian CTV isolates into two genotypes (CTV-1 and CTV-2) within the Piscihepevirus genus. Hepevirus genomes typically have three open reading frames but an ORF3 counterpart was not predicted in the Canadian CTV isolates. In vitro replication of a CTV-2 isolate produced cytopathic effects in the CHSE-214 cell line with similar amplification efficiency as CTV. Likewise, the morphology of the CTV-2 isolate resembled CTV, yet viral replication caused dilation of the endoplasmic reticulum lumen which was not previously observed. Controlled laboratory studies exposing sockeye (Oncorhynchus nerka), pink (O. gorbuscha), and chinook salmon (O. tshawytscha) to CTV-2 resulted in persistent infections without disease and mortality. Infected Atlantic salmon (Salmo salar) and chinook salmon served as hosts and potential reservoirs of CTV-2. The data presented herein provides the first in vitro and in vivo characterization of CTV-2 and reveals greater diversity of piscihepeviruses extending the known host range and geographic distribution of CTV viruses.
Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes?
Authors: Petrovic Fabijan Aleksandra , Aleksic Sabo Verica , Gavric Damir , Doffkay Zsolt , Rakhely Gábor , Knezevic Petar
Published: September 2021

Bordetella bronchiseptica is a respiratory animal pathogen that shows growing resistance to commonly used antibiotics, which has necessitated the examination of new antimicrobials, including bacteriophages. In this study, we examined the previously isolated and partially characterized B. bronchiseptica siphoviruses of the genus Vojvodinavirus (LK3, CN1, CN2, FP1 and MW2) for their ability to inhibit bacterial growth and biofilm, and we examined other therapeutically important properties through genomic analysis and lysogeny experiments. The phages inhibited bacterial growth at a low multiplicity of infection (MOI = 0.001) of up to 85% and at MOI = 1 for >99%. Similarly, depending on the phages and MOIs, biofilm formation inhibition ranged from 65 to 95%. The removal of biofilm by the phages was less efficient but still considerably high (40–75%). Complete genomic sequencing of Bordetella phage LK3 (59,831 bp; G + C 64.01%; 79 ORFs) showed integrase and repressor protein presence, indicating phage potential to lysogenize bacteria. Lysogeny experiments confirmed the presence of phage DNA in bacterial DNA upon infection using PCR, which showed that the LK3 phage forms more or less stable lysogens depending on the bacterial host. Bacterial infection with the LK3 phage enhanced biofilm production, sheep blood hemolysis, flagellar motility, and beta-lactam resistance. The examined phages showed considerable anti-B. bronchiseptica activity, but they are inappropriate for therapy because of their temperate nature and lysogenic conversion of the host bacterium.
Qualitative Assessment of Early Adverse Effects of Pfizer–BioNTech and Sinopharm COVID-19 Vaccines by Telephone Interviews
Authors: Abu-Halaweh Sami , Alqassieh Rami , Suleiman Aiman , Al-Sabbagh Mohammed Qussay , AbuHalaweh Maram , AlKhader Duaa , Abu-Nejem Rozan , Nabulsi Roa’a , Al-Tamimi Mohammad , Alwreikat Mallak , Alnouti Mazen , Suleiman Bayan , Yousef Moh’d , Jarbeh Mohammad El , Al-Shudifat Abdel-Ellah , Alqassieh Ahmad , Bsisu Isam
Published: September 2021

Vaccines are considered the best approach for countering the COVID-19 pandemic. In this study, we compared early side effects associated with vaccination with the Sinopharm and Pfizer–BioNTech COVID-19 vaccines. Participants of this observational cohort were interviewed based on semi-structured telephone interviews, with enquiries about side effects that developed after vaccination with each dose of these vaccines. Overall, 1004 participants were enrolled, of which 51.1% received Sinopharm vaccine and 48.9% received the Pfizer–BioNTech vaccine. After the first dose, 46.3% of participants had an adverse reaction, with injection site pain most commonly being reported (33.2%). Participants who received the Pfizer–BioNTech vaccine had significantly higher frequencies of all types of adverse reactions (p < 0.01), with no significant differences in the duration of adverse reactions between the two vaccines. Regarding the second dose, 48.6% of participants had adverse reactions, with injection site pain being most commonly reported (29%). Those who received the Pfizer vaccine reported higher frequencies of all adverse reactions (p < 0.01). However, a longer duration of adverse reactions was seen among Sinopharm vaccine recipients as compared to Pfizer–BioNTech vaccine recipients (p = 0.01). In conclusion, early adverse effects are reported following all types of vaccines but these are more likely to be encountered following the administration of new-generation vaccines. These side effects are mostly mild and treatable.
Willingness to Get the COVID-19 Vaccine among Residents of Slum Settlements
Authors: Aguilar Ticona Juan P. , Nery Nivison , Victoriano Renato , Fofana Mariam O. , Ribeiro Guilherme S. , Giorgi Emanuele , Reis Mitermayer G. , Ko Albert I. , Costa Federico
Published: September 2021

Slum residents are more vulnerable to COVID-19 infection. Without a specific treatment, vaccination became the main strategy against COVID-19. In this study, we determined the rate and factors associated with the willingness to get vaccinated against COVID-19 among slum residents and their main reasons associated with the vaccine intention. The study was conducted in Pau da Lima, a slum community in Salvador Brazil. In total, 985 residents were interviewed. Among them 66.0% (650/985) were willing to get vaccinated, 26.1% (257/985) were hesitant to take the vaccine and 7.9% (78/285) were not sure. The main reasons cited for vaccine hesitancy or being unsure were concerns about vaccine efficacy and potential side effects. In contrast, the main reasons cited for wanting the vaccine were the high incidence of COVID-19 cases and participants’ self-perception of their own health history. Multivariate analysis identified that COVID-19 vaccine hesitancy was associated with younger age and low social capital, summarized as low perceived importance of vaccination to protect one’s family, friends and community. Slum residents have been less willing to vaccinate than the general population. Social capital presents a critical opportunity in the design of communication campaigns to increase COVID-19 vaccine acceptance in slum settings.
Rhabdomyolysis Following Ad26.COV2.S COVID-19 Vaccination
Authors: Gelbenegger Georg , Cacioppo Filippo , Firbas Christa , Jilma Bernd
Published: September 2021

We report the case of a 19-year-old male who complained of myalgia, muscle weakness, and darkened urine two days after receiving his Ad26.COV2.S (Johnson & Johnson, New Brunswick, New Jersey, United States) COVID-19 vaccination. Blood examination revealed an increased creatine kinase (CK) level, and his urinary dipstick tested positive for blood, indicative of acute rhabdomyolysis. Serum creatinine levels were normal. Rhabdomyolysis due to strenuous physical activity was ruled out and further diagnostics excluded an autoimmune cause. Under repeated treatment with intravenous fluid resuscitation (outpatient treatment), his symptoms resolved and peak CK levels of 44,180 U/L returned to almost normal levels within two weeks. Rhabdomyolysis is a rare, potentially fatal vaccine-induced reaction. Further research is needed to better understand the underlying pathomechanism and to investigate whether subcutaneous injection of vaccines may be able to prevent rhabdomyolysis.
Vaccination against the Protozoan Parasite Histomonas meleagridis Primes the Activation of Toll-like Receptors in Turkeys and Chickens Determined by a Set of Newly Developed Multiplex RT-qPCRs
Authors: Mitra Taniya , Bramberger Beatrice , Bilic Ivana , Hess Michael , Liebhart Dieter
Published: September 2021

Histomonosis in turkeys and chickens is caused by the extracellular parasite Histomonas meleagridis, but the outcome of the disease varies depending on the host species. So far, studies on the immune response against histomonosis focus mainly on different traits of the adaptive immune system. Activation of toll like receptors (TLR) leads to the interplay between cells of innate and adaptive immunity with consequences on B and T cell clonal expansion. Therefore, the present investigation focused on the interaction of virulent and/or attenuated histomonads with the innate immune system of turkeys and chickens at 4, 10, 21 days post inoculation. The expression of TLRs (TLR1A, 1B, 2A, 2B, 3, 4, 5, 6(Tu), 7, 13(Tu) and 21(Ch)) and pro-inflammatory cytokines (IL1β and IL6) were analysed in caecum and spleen samples by RT-qPCR. Most frequent significant changes in expression levels of TLRs were observed in the caecum following infection with virulent parasites, an effect noticed to a lower degree in tissue samples from birds vaccinated with attenuated parasites. TLR1B, 2B and 4 showed a continuous up-regulation in the caecum of both species during infection or vaccination, followed by challenge with virulent parasites. Vaccinated birds of both species showed a significant earlier change in TLR expression following challenge than birds kept non-vaccinated but challenged. Expression of TLRs and pro-inflammatory cytokines were associated with severe inflammation of diseased birds in the local organ caecum. In the spleen, changes in TLRs and pro-inflammatory cytokines were less prominent and mainly observed in turkey samples. In conclusion, a detailed comparison of TLRs and pro-inflammatory cytokines of the innate immune system following inoculation with attenuated and/or virulent H. meleagridis of two avian host species provides an insight into regulative mechanisms of TLRs in the development of protection and limitation of the disease.
Incorporating the Cluster A and V1V2 Targets into a Minimal Structural Unit of the HIV-1 Envelope to Elicit a Cross-Clade Response with Potent Fc-Effector Functions
Authors: Sherburn Rebekah , Tolbert William D. , Gottumukkala Suneetha , Hederman Andrew P. , Beaudoin-Bussières Guillaume , Stanfield-Oakley Sherry , Tuyishime Marina , Ferrari Guido , Finzi Andrés , Ackerman Margaret E. , Pazgier Marzena
Published: September 2021

The generation of a potent vaccine for the prevention and/or control of HIV-1 has been unsuccessful to date, despite decades of research. Existing evidence from both infected individuals and clinical trials support a role for non-neutralizing or weakly neutralizing antibodies with potent Fc-effector functions in the prevention and control of HIV-1 infection. Vaccination strategies that induce such antibodies have proven partially successful in preventing HIV-1 infection. This is largely thought to be due to the polyclonal response that is induced in a vaccine setting, as opposed to the infusion of a single therapeutic antibody, which is capable of diverse Fc-effector functions and targets multiple but highly conserved epitopes. Here, we build on the success of our inner domain antigen, ID2, which incorporates conformational CD4-inducible (CD4i) epitopes of constant region 1 and 2 (C1C2 or Cluster A), in the absence of neutralizing antibody epitopes, into a minimal structural unit of gp120. ID2 has been shown to induce Cluster A-specific antibodies in a BALB/c mouse model with Fc-effector functions against CD4i targets. In order to generate an immunogen that incorporates both epitope targets implicated in the protective Fc-effector functions of antibodies from the only partially successful human vaccine trial, RV144, we incorporated the V1V2 domain into our ID2 antigen generating ID2-V1V2, which we used to immunize in combination with ID2. Immunized BALB/c mice generated both Cluster A- and V1V2-specific antibodies, which synergized to significantly improve the Fc-mediated effector functions compared to mice immunized with ID2 alone. The sera were able to mediate both antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). We therefore conclude that ID2-V1V2 + ID2 represents a promising vaccine immunogen candidate for the induction of antibodies with optimal Fc-mediated effector functions against HIV-1.
A Biological Study of Anisotropic Silver Nanoparticles and Their Antimicrobial Application for Topical Use
Authors: Thammawithan Saengrawee , Siritongsuk Pawinee , Nasompag Sawinee , Daduang Sakda , Klaynongsruang Sompong , Prapasarakul Nuvee , Patramanon Rina
Published: September 2021

The excessive use of antibiotics in both human and veterinary medicine has contributed to the development and rapid spread of drug resistance in bacteria. Silver nanoparticles (AgNPs) have become a tool of choice that can be used to treat these resistant bacteria. Several studies have shown that AgNPs have antibacterial and wound healing properties. In this study, we evaluated the biological activity of anisotropic AgNPs to develop an antimicrobial gel formulation for treating wound infections. We showed that some anisotropic AgNPs (S2) have an effective antibacterial activity against bacterial pathogens and low cytotoxicity to keratinocytes and fibroblasts in vitro. The MIC and MBC values were in the range of 2–32 µg/mL, and cytotoxicity had IC50 values of 68.20 ± 9.71 µg/mL and 68.65 ± 10.97 µg/mL against human keratinocyte and normal human dermal fibroblast cells, respectively. The anisotropic AgNPs (S2) were used as a gel component and tested for antibacterial activity, including long-term protection, compared with povidone iodine, a common antiseptic agent. The results show that the anisotropic AgNPs can inhibit the growth of most tested bacterial pathogens and provide protection longer than 48 h, whereas povidone iodine only inhibits the growth of some bacteria. This study suggests that anisotropic AgNPs could be used as an alternative antimicrobial agent for treating bacterial skin infection and as a wound healing formulation.
The Effect of Soil Conservation Measures on Runoff, Soil Erosion, TN, and TP Losses Based on Experimental Runoff Plots in Northern China
Authors: Fang Haiyan
Published: September 2021

Total nitrogen (TN) and total phosphorous (TP) are the main pollutants affecting the water quality of the Miyun Reservoir, Beijing. However, few studies have been conducted on their responses to implemented soil conservation measures at a slope scale in northern China. To explore the impact of soil conservation measures on TN and TP losses, field monitored data from 18 runoff plots under natural rainfalls were used to analyze the changing characteristics of runoff, soil loss, and nutrient losses during 2014–2019. The results indicated that runoff, soil erosion, as well a TN and TP losses from the plots varied significantly, depending on land use and soil conservation measures. Bare plots suffered the highest soil, TN, and TP losses, followed by cultivated plots without soil conservation measures, cultivated plots with contour tillage, and other plots. Event-averaged runoff and soil loss rates ranged from 0 to 7.9 mm and from 0 to 444.4 t km−2 yr−1, and event-averaged TN and TP losses from cultivated plots were the highest, with values of 39.8 and 3.0 kg km−2, respectively. Bare and cultivated plots were the main sediment and nutrient sources. Among the cultivated plots, the terraced plot had the lowest soil and nutrient losses. The vegetated plots had insignificantly lower soil and nutrient losses. Most TN and TP were lost in particulate status from the plots, especially from the plots with soil conservation measures. Soil conservation measures can effectively prevent TN and TP losses. To guarantee water resource use, contour tillage is preferred for the bare and cultivated lands in the study region.
Evaluation of Land-Use Changes Impact on Watershed Health Using Probabilistic Approaches
Authors: Lee Jiwan , Chung Jeehun , Woo Soyoung , Lee Yonggwan , Jung Chunggil , Park Daeryong , Kim Seongjoon
Published: September 2021

This study evaluated watershed health (WH) change using reference values for environmental changes at various times. Land use in 1985 was defined as the reference value under the most natural conditions, and the WH for the years 1995 to 2019 was calculated in comparison to 1985. The proposed method was used to assess the WH of 78 standard subbasins in South Korea’s Geum River Basin (GRB), where complex land-use change has occurred since 1995. For evaluating hydrology and water quality (WQ) health index, Soil and Water Assessment Tool (SWAT) and four land-use maps (1985, 1995, 2008, and 2019) were used to simulate the hydrology and WQ. A multivariate normal distribution (MND) from poor (0) to good (1) was used to assess WH based on SWAT modeling results. Based on the reference value, the WQ health from 1995 to 2019 changed to within 0.1, while the range of changes in the hydrology index was analyzed over 0.18. As a result of WH changes from 1985 to 2019, hydrological health deteriorated in high-density urbanized subbasins, while WQ health deteriorated in upland-cultivation-increased subbasins. This study provides useful information for recognizing potential WH issues related to long-term environmental changes.
Revisiting the Gage–Bidwell Law of Dilution in Relation to the Effectiveness of Swimming Pool Filtration and the Risk to Swimming Pool Users from Cryptosporidium
Authors: Simmonds Lester P. , Simmonds Guy E. , Wood Martin , Marjoribanks Tim I. , Amburgey James E.
Published: September 2021

The transfer of water from a swimming pool to the treatment location is key in determining the effectiveness of water treatment by filtration in removing turbidity and managing the risk from particulate material, including microbial pathogens, such as Cryptosporidium spp. A key recommendation for pool operators when dealing with an accidental faecal release (the likely main source of high Cryptosporidium oocyst concentrations in pools) is that the pool water should be filtered for at least six turnover cycles prior to use. This paper briefly outlines the theoretical basis of what has become known as the Gage–Bidwell Law of Dilution, which provides a basis for this recommendation, and extends the idea to account for the impact of filter efficiency. The Gage–Bidwell Law reveals that for each pool turnover 63% of the water resident in the pool at the start of the turnover period will have been recirculated. Building on this, we demonstrate that both filter efficiency and water-turnover time are important in determining filtration effectiveness and can be combined through a single parameter we term ‘particle-turnover’. We consider the implications of the Gage–Bidwell Law (as referred to in the original 1926 paper) for the dynamics of the ‘dirt’ content of pool water, whether in terms of a specific particle size range (e.g., Cryptosporidium oocysts) or turbidity.
Computational Fluid Dynamics Simulation of Suspended Solids Transport in a Secondary Facultative Lagoon Used for Wastewater Treatment
Authors: Zapata Rivera Andres Mauricio , Ducoste Joel , Peña Miguel Ricardo , Portapila Margarita
Published: September 2021

The facultative lagoon hydrodynamics has been evaluated using computational fluid dynamics tools, however, little progress has been made in describing the transport of suspended solids within these systems, and their effects on fluid hydrodynamics. Traditionally, CFD models have been built using pure water. In this sense, the novelty in this study was to evaluate the influence of suspended solids transport on the hydrodynamics of an facultative lagoon. Two three-dimensional CFD models were developed, a single-phase model (pure water) and a two-phase model (water and suspended solids), for a conventional FL in Ginebra, Valle del Cauca, Colombia. Model results were compared with experimental tracer studies, displaying different tracer dispersion characteristics. Differences in the fluid velocity field were identified when suspended solids were added to the simulation. The fluid velocities in the single-phase model were greater than the fluid velocities obtained in the two-phase model, (0.127 m·s−1 and 0.115 m·s−1, respectively). Additionally, the dispersion number of each model showed that the single-phase model (0.478) exhibited a better behavior of complete mixing reactor than the two-phase model (0.403). These results can be attributed to the effect of the drag and slip forces of the solids on the velocity of the fluid. In conclusion, the fluid of FL in these models is better represented as a two-phase fluid in which the particle–fluid interactions are represented by drag and slip forces.
Future Changes in Precipitation Extremes over East Africa Based on CMIP6 Models
Authors: Ayugi Brian , Dike Victor , Ngoma Hamida , Babaousmail Hassen , Mumo Richard , Ongoma Victor
Published: September 2021

This paper presents an analysis of projected precipitation extremes over the East African region. The study employs six indices defined by the Expert Team on Climate Change Detection Indices to evaluate extreme precipitation. Observed datasets and Coupled Model Intercomparison Project Phase six (CMIP6) simulations are employed to assess the changes during the two main rainfall seasons: March to May (MAM) and October to December (OND). The results show an increase in consecutive dry days (CDD) and decrease in consecutive wet days (CWD) towards the end of the 21st century (2081–2100) relative to the baseline period (1995–2014) in both seasons. Moreover, simple daily intensity (SDII), very wet days (R95 p), very heavy precipitation >20 mm (R20 mm), and total wet-day precipitation (PRCPTOT) demonstrate significant changes during OND compared to the MAM season. The spatial variation for extreme incidences shows likely intensification over Uganda and most parts of Kenya, while a reduction is observed over the Tanzania region. The increase in projected extremes may pose a serious threat to the sustainability of societal infrastructure and ecosystem wellbeing. The results from these analyses present an opportunity to understand the emergence of extreme events and the capability of model outputs from CMIP6 in estimating the projected changes. More studies are recommended to examine the underlying physical features modulating the occurrence of extreme incidences projected for relevant policies.