bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk Assessment of Heavy Metals in Basmati Rice: Implications for Public Health
Authors: Tariq Farah , Wang Xiukang , Saleem Muhammad Hamzah , Khan Zafar Iqbal , Ahmad Kafeel , Saleem Malik Ifra , Munir Mudasra , Mahpara Shehzadi , Mehmood Naunain , Ahmad Tasneem , Memona Hafsa , Ugulu Ilker , Fiaz Sajid , Ali Shafaqat
Published: August 2021

Basmati rice is increasingly recognized and consumed in different parts of the world due to its different tastes and nutritional properties. This research focused on determining the cadmium (Cd), cobalt (Co), Copper (Cu), iron (Fe), manganese (Mn), nickel (Ni) and zinc (Zn) content in locally grown basmati rice in Pakistan and assessing the risks of these values to human health. Root, shoot and grain samples of basmati rice were taken, along with soil samples from the five regions studied. Metal mean concentrations (mg/kg) in grains fluctuated from 2.70 to 9.80 for Cd, 4.80 to 9.85 for Zn, 1.16 to 1.46 for Cu, 1.84 to 10.86 for Co, 2.05 to 13.07 for Fe, 5.03 to 11.11 for Mn and 3.24 to 13.28 for Ni, respectively. All metal values were within permissible limits except for Cd. The enrichment factor for Cd was highest among all sites. Cobalt and zinc had the highest bioaccumulation factor and translocation factor. The highest enrichment factor was noticed for Cd and the lowest for Cu. The health risk index at all examined sites was less than one. Consistent examination is recommended to limit health hazards instigated by the use of rice polluted with a greater concentration of Cd.
Voluntary Reporting in Decarbonizing Container Shipping: The Clean Cargo Case
Authors: Godet Amandine , Panagakos George , Barfod Michael Bruhn
Published: August 2021

Led by the UN’s International Maritime Organization (IMO) and the EU, the shipping industry struggles to reduce its greenhouse gas (GHG) emissions to align with the Paris Agreement. Clean Cargo, the leading voluntary buyer–supplier forum for sustainability in the cargo shipping industry, developed some years ago a methodology to calculate and report the GHG emissions from containerships. The recently introduced carbon emission requirements by the IMO and EU have reinforced the members’ interest in a new Clean Cargo reporting mechanism that enables a more effective and efficient monitoring of the decarbonization progress. A better understanding of the user needs accompanied by due consideration to the regulatory environment and the technological advances are key to build this new framework. This paper builds on the case of the Clean Cargo initiative to (1) identify the stakeholders’ expectations and motivations for voluntary disclosure of environmental information, and (2) discuss the governance challenges of voluntary initiatives. A questionnaire was designed and deployed to investigate the current uses of Clean Cargo data and the information sharing among different stakeholders. Voluntary schemes can speed up the decarbonization process by proposing standards accepted by all actors of the global value chain. Clean Cargo members envision reporting on absolute GHG emissions per shipment as the way forward.
Early Bird Scheme for Parking Management: How Does Parking Play a Role in the Morning Commute Problem
Authors: Zhang Zipeng , Zhang Ning
Published: August 2021

This paper extended the Vickrey’s point-queue model to study the early bird parking mechanism during morning commute peak hours. We not only investigated how commuters choose departure times in view of morning commute traffic congestion and the discounted early bird parking fee, but also analyzed the conditions which are determined for the existence of the user equilibrium in the analysis model provided in this paper. Moreover, the tendency of the total queuing time and the incremental parking pricing revenue was derived along with the different choice strategy between early bird parkers (ERPs) and regular parkers (RPs). The results showed that the number of commuters was jointly determined by the desired time and the bottleneck capacity for different schedules. Additionally, the method of fare incentive showed a better effect on reducing queue than the initial no-incentive method with the instantaneous travel demand. Most importantly, the incremental parking revenue can be increased by properly adjusting the parking pricing gap between ERPs and RPs. Our research not only provided several important propositions for the early bird parking mechanism but also included the optimal solutions for optimal parking pricing and schedule gap in two groups of parkers. This work is expected to promote the development of early bird parking to mitigate morning commute traffic congestion and motivate the related research of schedule coordination for regulating parking choice behavior in morning peak hours.
Biodiversity Monitoring in Long-Distance Food Supply Chains: Tools, Gaps and Needs to Meet Business Requirements and Sustainability Goals
Authors: Beck-O’Brien Meghan , Bringezu Stefan
Published: August 2021

Rampant loss of biodiversity and ecosystem services undermines the resilience of food systems. Robust knowledge on impacts is the first step to taking action, but long-distance food supply chains and indirect effects on and around farms make understanding impacts a challenge. This paper looks at the tools available for businesses in the food industry, especially retailers, to monitor and assess the biodiversity performance of their products. It groups tools according to their general scope to evaluate what is monitored (processes on-site, pressures on landscapes, impacts on species), at what scale (specific products, company performance, country-wide consumption levels), and compared to which baseline (pristine nature, alternative scenarios, governance targets). Altogether we find major gaps in the criteria for biodiversity or the criteria is weak in certification and standards, business accounting and reporting systems, and scientific modelling and analysis (biodiversity footprints). At the same time, massive investments have been made to strengthen existing tools, develop new ones, increase uptake and improve their effectiveness. We argue that business can and must take a leading role toward mitigating biodiversity impacts in partnership with policy makers and customers. Zero-deforestation commitments, for example, will need to be upheld by supporting changed practices in consumption (e.g., choice editing) and combating degradation within agricultural systems will require a shift toward more regenerative forms of farming (e.g., with norms embedded in robust standard systems). Operational targets are integral to monitoring biodiversity performance across all scales.
Spatial-Temporal Evolution and Relationship between Urbanization Level and Ecosystem Service from a Dual-Scale Perspective: A Case Study of the Pearl River Delta Urban Agglomeration
Authors: Mao Yuanyuan , Hou Lingli , Zhang Zhengdong
Published: August 2021

Since the beginning of the 21st century, urbanization has brought about dramatic changes in population, life, and economy, while having a significant impact on the distribution of ecosystem service. As research on the relationship between urbanization and ecosystem service has gradually specified, we decided to explore it at different scales. In this paper, we quantified and mapped the spatial–temporal evolution and relationship between urbanization and ecosystem service value in the Pearl River Delta Urban Agglomeration from 2000 to 2019 based on a dual-scale perspective of county and 3 km × 3 km raster. Our results show that the overall trend of urbanization level and ecosystem service value was increasing. Urbanization and ecosystem service value at the county scale showed a negative spatial correlation, while it was not significant at the raster scale. The “high–high” agglomeration was more concentrated, while the other three “low–low”, “low–high” and “high–low” agglomerations were more dispersed. Our findings suggest it is crucial to identify the key factors of small urban areas to grasp the development mechanism in the urbanization process and maintain the balance of the ecosystem.
The Impact of Information Technology and Sustainable Strategies in Hotel Branding, Evidence from the Greek Environment
Authors: Varelas Sotirios , Karvela Panagiota , Georgopoulos Nikolaos
Published: August 2021

Information Systems, Sustainable Development and Hotel Branding are the main study areas of this specific research. In recent years, many technologies have been which have started to be implemented in the hospitality industry, but the full potential of these technologies has not yet been analyzed in order to understand how they could help companies to develop branding strategies and increase the customer’s loyalty and business performance. Moreover, due to the pandemic crisis due to COVID-19, hotel companies have to manage a new crisis, which affects both the economic and social pillars of their sustainable development. Therefore, the hospitality industry must be more flexible in adopting information technologies and sustainable philosophies, firstly for their own survival and secondly to strengthen their position inside the task environment. The methodology approach was based both on the literature review and qualitative methodology, which was conducted through questionnaires. The aim of this research is to analyze the above concepts and see how this combination could lead the hotel companies to develop a competitive advantage inside their task environment. The findings of this research concern the region of Greece. They reveal that there is a strong correlation among the above concepts, and each company should start to adopt sustainable philosophy, use information technologies, and develop new branding strategies.
Urban Data Dynamics: A Systematic Benchmarking Framework to Integrate Crowdsourcing and Smart Cities’ Standardization
Authors: Moustaka Vaia , Maitis Antonios , Vakali Athena , Anthopoulos Leonidas G.
Published: August 2021

Urbanization and knowledge economy have highly marked the new millennium. Urbanization brings new challenges which can be addressed by the knowledge economy, which opens up scientific and technical innovation opportunities. The enhancement of cities’ intelligence has heavily impacted city transformation and sustainable decision-making based on urban data knowledge extraction. This work is motivated by the strong demand for robust standardization efforts to steer and measure city performance and dynamics, given the growing tendency of conventional cities’ transformation into smart and resilient ones. This paper revises the earlier so-called “cityDNA” framework, which was designed to detect the interrelations between the six smart city dimensions, such that a city’s profile and capacities are recognized in a systematic manner. The updated framework implements the widely accepted smart city (ISO 37120:2018) standard, along with an adaptive Web service, which processes urban data and visualizes the city’s profile to facilitate decision-making. The proposed framework offers a solid benchmarking service, at which the value of crowdsourced data is exploited for the production of urban knowledge and city transformation empowerment. The proposed benchmarking approach is tested and validated through relevant case studies and a proof-of-concept scenario, in which open data and crowdsourced data are exploited. The outcomes revealed that cities should intensify their KPI-driven data production and exploitation along with a set of solid standards for cities to enable cities with customizable scenarios enriched with indicators that reflect each city’s vibrancy.
Sorting Analysis of Household Food Waste—Development of a Methodology Compatible with the Aims of SDG12.3
Authors: Okayama Tomoko , Watanabe Kohei , Yamakawa Hajime
Published: August 2021

Target 12.3 of the United Nations Sustainable Development Goals (SDGs) calls for halving per capita global food waste at the retail and consumer levels, by 2030. The Food Waste Index is suggested as a methodology for grasping the situation. This paper focuses on the consumer level (household food waste). We argue that in order for generating useful information for devising and implementing effective measures for reducing food waste, it should be measured at Level 3 of the Food Waste Index, based on sorting analysis of generated waste, and making a distinction between avoidable and non-avoidable food waste. Furthermore, a breakdown by subcategories that reflect the flow of food in the household could help identify target behaviours. We have developed a categorisation scheme that is internationally agreeable and adoptable, and (1) generates useful information for policy-making and for tackling with reduction of food waste, (2) makes clear the concept of avoidable food waste, and (3) is practical and does not overcomplicate the work of grasping the situation of food wastage. Results of workshops regarding this scheme suggest that the scheme satisfies the criteria. This scheme has been applied to a few sorting analyses of household food waste in Japan, and their results are compared.
COVID-19 Pandemic: Is the Crypto Market a Safe Haven? The Impact of the First Wave
Authors: Vukovic Darko , Maiti Moinak , Grubisic Zoran , Grigorieva Elena , Frömmel Michael
Published: August 2021

The present study investigated whether the crypto market is a safe haven. The study argues that during the first wave of the COVID-19 crisis, gold and oil, as typical global commodities, could have been diversifiers. The study developed a unique COVID-19 global composite index that measures COVID-19 pandemic time-variant movements on each day. The study used OLS (ordinary least squares), quantile, and robust regressions to check whether the COVID-19 crisis has had any significant direct influence on the crypto market. The OLS, quantile, and robust regressions estimates confirmed that there was no statistically significant direct influence of the COVID-19 crisis on the crypto market in the first wave period. However, the study found spillovers from risky assets (S&P 500) on the crypto market, with Tether as an exception. Due to this special characteristic, Tether might present a safe haven within the crypto market.
Environmental Assessment of University Campuses: The Case of the University of Navarra in Pamplona (Spain)
Authors: Arias Alba , Leon Iñigo , Oregi Xabat , Marieta Cristina
Published: August 2021

Current European environmental sustainability standards call for achieving a reduction in energy consumption and CO2 emissions for a horizon set in the year 2050. It has been verified that buildings and cities have a higher incidence in this regard. It is necessary to have tools for initial assessment that can quickly analyse whether the improvement scenarios put forward by different organisations and governments will be able to meet the goals set at European level. Universities are an important factor for the intended change and therefore offer an excellent environment for testing such tools. A case study focusing on a university in northern Spain is presented, through an evaluation tool using 3D models including life-cycle assessment. Different reform scenarios are evaluated for two key years, 2030 and 2050. The novelty lies in considering, not only the impact of the operational phase but also the impact of the different stages of the life cycle and processes, obtaining an impact value closer to reality. The results indicate that, even with major retrofitting and adaptation efforts, the European targets are difficult to achieve by 2050. Moreover, solutions such as biomass help to achieve greenhouse gas reductions but not to improve energy efficiency.
Trends and Development of the Directors’ Duty of Loyalty in China: A Case Analysis
Authors: Wen Shuangge , Zhao Jingchen
Published: August 2021

Covering a central theme in corporate law development, this paper discusses the pragmatic utility of the common-law-originated duty of loyalty of company directors in the civil law context of China. The reception of legal transplantation in a host environment remains a contentious theme, and it seems to be an opportune time to study relevant cases that have been adjudicated since China’s statutory inauguration of the directors’ duty of loyalty in 2005, in the sense that more than 10 years of practice has resulted in ample evidence on the practical effects of this transplanted duty. Through an analysis of 526 cases on the basis of eight attributes, we discovered some commendable features, including increasing accessibility of the law and a differentiation of various types of directors’ duties of loyalty. Meanwhile, the selective adoption norm customary to Chinese culture has to a certain extent compromised the intended goals of greater legislative clarity, judicial consistency and in turn balanced and sustainable businesses, demonstrated in several incompatibilities between transplanted duties and domestic legal institutions. Reshaping the conventional transplantation ideal that commercial laws are easily transferable, the paper suggests the construction of a broad collateral regime for greater congruence between laws and existing institutions.
Family Conditions and the Accessibility of Online Education: The Digital Divide and Mediating Factors
Authors: Gu Jiafeng
Published: August 2021

This study is an exploration of the digital divide between urban and rural areas, and it was conducted to assess the impact of the minimum living guarantee system on online education in China. The results of the research showed that 83.38% of students in low-income families have been able to participate in online education at home during the pandemic, while 16.62% of students in low-income families have been unable to do so. The absence of computers, smartphones, and broadband Internet access in low-income households reduces the likelihood of children being able to participate in online education at home. In terms of accessing online education at home, students from urban areas have obvious advantages over those from rural ones, and students from minimum living guarantee families have obvious advantages over those from marginal minimum living guarantee ones. This study also showed that the presence of online education-related amenities, including computers, smartphones, and Internet access, mediates the relationship between the subsistence allowance system, Hukou, and accessibility of online education. To address this issue, this paper includes suggestions for bridging the digital divide in online education.
Parametric Design Structures in Low Rise Buildings in Relation to the Urban Context in UAE
Authors: Bande Lindita , Alshamsi Abeer , Alhefeiti Anoud , Alderei Sarah , Shaban Sebah , Albattah Mohammed , Scoppa Martin D.
Published: August 2021

The city of Al Ain (Abu Dhabi, UAE) has a mainly low rise residential buildings. Villas as part of a compound or separate units represent the majority of the residential areas in the city. Due to the harsh hot arid climate of Al Ain, the energy demand for the cooling load is quite high. Therefore, it is relevant finding new retrofit strategies that are efficient in reducing the cooling load of the villas. The aim of this study is to analyze one particular strategy (parametric shading structure) in terms of design, construction, cost, energy impact on the selected villa. The main data for this study is taken from the local sources. There are six steps followed in this analysis: case study analysis; climate analysis; parametric structure and PV panels; building energy consumption and outdoor thermal comfort; modelling, simulation, and validation; materials, construction, and cost evaluation. The model of the villa was validated for the full year 2020 based on the electricity bills obtained. After adding the parametric design structure, the reduction after shading is approximately 10%. Meanwhile the UTCI (Universal Thermal Climate Index) dropped from extreme heat stress to strong heat stress (average for the month of March and September). These findings are promising in the retrofit industry due to the advanced calculations used to optimize the parametric design structure.
A Sustainable Multicriteria Decision Framework for Obsolescence Resolution Strategy Selection
Authors: Zaabar Imen , Arango-Miranda Raul , Beauregard Yvan , Paquet Marc
Published: August 2021

Parts obsolescence has an important impact on the product life cycle, the manufacturing system and the environment leading to operational, logistical, reliability and cost implications. While current resolution models are cost-oriented, multiple studies have revealed that technological obsolescence is strongly involved in the electronic waste problem. In this study, based on academic literature and expert opinions, a sustainable decision framework for obsolescence resolution strategy (ORS) selection is proposed. It consists of economic, environmental, social and technological dimensions, integrating a total of fifteen criteria. Multicriteria decision-making (MCDM) methods are suggested to select the most sustainable solution. A case study was performed where the criteria weights and the alternatives performance were judged by five experts from the fields of environment, economy, human resources and obsolescence and operations management. Results from different MCDM methods were compared to the actual decision to evaluate their effectiveness. Using the suggested framework improved the decision process as integrating sustainability had a drastic impact on the selected strategy and consequently on the company’s performance. In addition to its managerial insights, this paper provides a new research perspective to sustainable and robust obsolescence management to effectively handle the increasing number and severity of obsolete components.
Mineralization of Farm Manures and Slurries under Aerobic and Anaerobic Conditions for Subsequent Release of Phosphorus and Sulphur in Soil
Authors: Islam Mohammad Rafiqul , Bilkis Sultana , Hoque Tahsina Sharmin , Uddin Shihab , Jahiruddin Mohammad , Rahman Mohammad Mazibur , Siddique Abu Bakkar , Hossain Mohammad Anwar , Danso Marfo Theodore , Danish Subhan , Datta Rahul
Published: August 2021

A good understanding of nutrient release from manure or compost after application through mineralization is important to assure meeting the nutrient demand of crops, to secure timely fertilizer application and to enhance nutrient use efficiency. The current study was done to evaluate phosphorus (P) and sulphur (S) release patterns from different types of manures viz. cow dung, cow dung slurry, tricho-compost, vermicompost, poultry manure, poultry manure slurry and mungbean residues. The mineralization study was performed under aerobic (field capacity) and anaerobic (waterlogging) conditions for 180 days at 25 ± 1 °C in the laboratory. The release of P and S showed the highest values within 75–180 and 75–150 days, respectively, and was always higher in aerobic conditions than in anaerobic conditions. The first-order kinetic cumulative model was a good fit for mineralization, which was significantly influenced by manure type, soil moisture level and incubation period. Poultry manure slurry exerted the highest P and S release under both moisture conditions. Both slurries showed higher potential mineralization, with a lower rate constant for these elements compared to that in their manure states. Hence, appropriate manures should be chosen and applied in the proper quantity to provide exact amounts of nutrients, to increase crops nutrient use efficiency and to formulate correct fertilizer recommendations.
Human Appropriation of Net Primary Production: From a Planet to a Pixel
Authors: Paudel Suman , Ovando-Montejo Gustavo A. , Lant Christopher L.
Published: August 2021

Human appropriation of net primary production (HANPP) is a substantial improvement upon 20th century attempts at developing an ecological footprint indicator because of its measurability in relation to net primary production, its close relationship to other key footprint measures, such as carbon and water, and its spatial specificity. This paper explores HANPP across four geographical scales: through literature review, the planet; through reanalysis of existing data, variations among the world’s countries; and through novel analyses, U.S. counties and the 30 m pixel scale for one U.S. county. Results show that HANPP informs different sustainability narratives at different scales. At the planetary scale, HANPP is a critical planetary limit that improves upon areal land use indicators. At the country macroscale, HANPP indicates the degree to which meeting the needs of the domestic population for provisioning ecosystem services (food, feed, biofiber, biofuel) presses against the domestic ecological endowment of net primary production. At the county mesoscale, HANPP reveals the dependency of metropolitan areas upon regional specialized rural forestry and agroecosystems to which they are teleconnected through trade and transport infrastructures. At the pixel microscale, HANPP provides the basis for deriving spatial patterns of remaining net primary production upon which biodiversity and regulatory and cultural ecosystem services are dependent. HANPP is thus a sustainability indicator that can fulfill similar needs as carbon, water and other footprints.
Logical Contradictions in the One-Way ANOVA and Tukey–Kramer Multiple Comparisons Tests with More Than Two Groups of Observations
Authors: Gurvich Vladimir , Naumova Mariya
Published: August 2021

We show that the one-way ANOVA and Tukey–Kramer (TK) tests agree on any sample with two groups. This result is based on a simple identity connecting the Fisher–Snedecor and studentized probabilistic distributions and is proven without any additional assumptions; in particular, the standard ANOVA assumptions (independence, normality, and homoscedasticity (INAH)) are not needed. In contrast, it is known that for a sample with k>2 groups of observations, even under the INAH assumptions, with the same significance level α, the above two tests may give opposite results: (i) ANOVA rejects its null hypothesis H0A:μ1=…=μk, while the TK one, H0TK(i,j):μi=μj, is not rejected for any pair i,j∈{1,…,k}; (ii) the TK test rejects H0TK(i,j) for a pair (i,j) (with i≠j), while ANOVA does not reject H0A. We construct two large infinite pseudo-random families of samples of both types satisfying INAH: in case (i) for any k≥3 and in case (ii) for some larger k. Furthermore, case (ii) ANOVA, being restricted to the pair of groups (i,j), may reject equality μi=μj with the same α. This is an obvious contradiction, since μ1=…=μk implies μi=μj for all i,j∈{1,…,k}. Such contradictions appear already in the symmetric case for k=3, or in other words, for three groups of d,d, and c observations with sample means +1,−1, and 0, respectively. We outline conditions necessary and sufficient for this phenomenon. Similar contradictory examples are constructed for the multivariable linear regression (MLR). However, for these constructions, it seems difficult to verify the Gauss–Markov assumptions, which are standardly required for MLR. Mathematics Subject Classification: 62 Statistics.
Formaldehyde in Hospitals Induces Oxidative Stress: The Role of GSTT1 and GSTM1 Polymorphisms
Authors: Ghelli Federica , Bellisario Valeria , Squillacioti Giulia , Panizzolo Marco , Santovito Alfredo , Bono Roberto
Published: August 2021

Despite the toxicity and health risk characteristics of formaldehyde (FA), it is currently used as a cytological fixative and the definition of safe exposure levels is still a matter of debate. Our aim was to investigate the alterations in both oxidative and inflammatory status in a hospital working population. The 68 workers recruited wore a personal air-FA passive sampler, provided a urine sample to measure 15-F2t-Isoprostane (15-F2t-IsoP) and malondialdehyde (MDA) and a blood specimen to measure tumour necrosis factor α (TNFα). Subjects were also genotyped for GSTT1 (Presence/Absence), GSTM1 (Presence/Absence), CYP1A1 exon 7 (A > G), and IL6 (−174, G > C). Workers were ex post split into formalin-employers (57.3 μg/m3) and non-employers (13.5 μg/m3). In the formalin-employers group we assessed significantly higher levels of 15-F2t-IsoP, MDA and TNFα (<0.001) in comparison to the non-employers group. The air-FA levels turned out to be positively correlated with 15-F2t-IsoP (p = 0.027) and MDA (p < 0.001). In the formalin-employers group the MDA level was significantly higher in GSTT1 Null (p = 0.038), GSTM1 Null (p = 0.031), and CYP1A1 exon 7 mutation carrier (p = 0.008) workers, compared to the wild type subjects. This study confirms the role of FA in biomolecular profiles alterations, highlighting how low occupational exposure can also result in measurable biological outcomes.
The Natterin Proteins Diversity: A Review on Phylogeny, Structure, and Immune Function
Authors: Lima Carla , Disner Geonildo Rodrigo , Falcão Maria Alice Pimentel , Seni-Silva Ana Carolina , Maleski Adolfo Luis Almeida , Souza Milena Marcolino , Reis Tonello Mayara Cristina , Lopes-Ferreira Monica
Published: August 2021

Since the first record of the five founder members of the group of Natterin proteins in the venom of the medically significant fish Thalassophryne nattereri, new sequences have been identified in other species. In this work, we performed a detailed screening using available genome databases across a wide range of species to identify sequence members of the Natterin group, sequence similarities, conserved domains, and evolutionary relationships. The high-throughput tools have enabled us to dramatically expand the number of members within this group of proteins, which has a remote origin (around 400 million years ago) and is spread across Eukarya organisms, even in plants and primitive Agnathans jawless fish. Overall, the survey resulted in 331 species presenting Natterin-like proteins, mainly fish, and 859 putative genes. Besides fish, the groups with more species included in our analysis were insects and birds. The number and variety of annotations increased the knowledge of the obtained sequences in detail, such as the conserved motif AGIP in the pore-forming loop involved in the transmembrane barrel insertion, allowing us to classify them as important constituents of the innate immune defense system as effector molecules activating immune cells by interacting with conserved intracellular signaling mechanisms in the hosts.
Clinically Important Phleboviruses and Their Detection in Human Samples
Authors: Lambert Amy J. , Hughes Holly R.
Published: August 2021

The detection of phleboviruses (family: Phenuiviridae) in human samples is challenged by the overall diversity and genetic complexity of clinically relevant strains, their predominantly nondescript clinical associations, and a related lack of awareness among some clinicians and laboratorians. Here, we seek to inform the detection of human phlebovirus infections by providing a brief introduction to clinically relevant phleboviruses, as well as key targets and approaches for their detection. Given the diversity of pathogens within the genus, this report focuses on diagnostic attributes that are generally shared among these agents and should be used as a complement to, rather than a replacement of, more detailed discussions on the detection of phleboviruses at the individual virus level.
Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins
Authors: Leavitt Justin C. , Gilcrease Eddie B. , Woodbury Brianna M. , Teschke Carolyn M. , Casjens Sherwood R.
Published: August 2021

Tailed double-stranded DNA bacteriophages inject some proteins with their dsDNA during infection. Phage P22 injects about 12, 12, and 30 molecules of the proteins encoded by genes 7, 16 and 20, respectively. After their ejection from the virion, they assemble into a trans-periplasmic conduit through which the DNA passes to enter the cytoplasm. The location of these proteins in the virion before injection is not well understood, although we recently showed they reside near the portal protein barrel in DNA-filled heads. In this report we show that when these proteins are missing from the virion, a longer than normal DNA molecule is encapsidated by the P22 headful DNA packaging machinery. Thus, the ejection proteins occupy positions within the virion that can be occupied by packaged DNA when they are absent.
Modified-Live Feline Calicivirus Vaccination Reduces Viral RNA Loads, Duration of RNAemia, and the Severity of Clinical Signs after Heterologous Feline Calicivirus Challenge
Authors: Spiri Andrea M. , Riond Barbara , Stirn Martina , Novacco Marilisa , Meli Marina L. , Boretti Felicitas S. , Herbert Imogen , Hosie Margaret J. , Hofmann-Lehmann Regina
Published: August 2021

Feline calicivirus (FCV) is a common cat virus causing clinical signs such as oral ulcerations, fever, reduced general condition, pneumonia, limping and occasionally virulent-systemic disease. Efficacious FCV vaccines protect against severe disease but not against infection. FCV is a highly mutagenic RNA virus whose high genetic diversity poses a challenge in vaccine design. The use of only one modified-live FCV strain over several decades might have driven the viral evolution towards more vaccine-resistant variants. The present study investigated the clinical signs, duration, and amount of FCV shedding, RNAemia, haematological changes and acute phase protein reaction in SPF cats after subcutaneous modified-live single strain FCV vaccination or placebo injection and two subsequent oronasal heterologous FCV challenge infections with two different field strains. Neither clinical signs nor FCV shedding from the oropharynx and FCV RNAemia were detected after vaccination. After the first experimental infection, vaccinated cats had significantly lower clinical scores, less increased body temperature and lower acute phase protein levels than control cats. The viral RNA loads from the oropharynx and duration and amount of RNAemia were significantly lower in the vaccinated animals. No clinical signs were observed in any of the cats after the second experimental infection. In conclusion, FCV vaccination was beneficial for protecting cats from severe clinical signs, reducing viral loads and inflammation after FCV challenge.
Severe SARS-CoV-2 Infection in a Cat with Hypertrophic Cardiomyopathy
Authors: Carvallo Francisco R. , Martins Mathias , Joshi Lok R. , Caserta Leonardo C. , Mitchell Patrick K. , Cecere Thomas , Hancock Sandy , Goodrich Erin L. , Murphy Julia , Diel Diego G.
Published: August 2021

Coronavirus disease 19 (COVID-19), has claimed millions of human lives worldwide since the emergence of the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019. Notably, most severe and fatal SARS-CoV-2 infections in humans have been associated with underlying clinical conditions, including diabetes, hypertension and heart diseases. Here, we describe a case of severe SARS-CoV-2 infection in a domestic cat (Felis catus) that presented with hypertrophic cardiomyopathy (HCM), a chronic heart condition that has been described as a comorbidity of COVID-19 in humans and that is prevalent in domestic cats. The lung and heart of the affected cat presented clear evidence of SARS-CoV-2 replication, with histological lesions similar to those observed in humans with COVID-19 with high infectious viral loads being recovered from these organs. The study highlights the potential impact of comorbidities on the outcome of SARS-CoV-2 infection in animals and provides important information that may contribute to the development of a feline model with the potential to recapitulate the clinical outcomes of severe COVID-19 in humans.
The Interplay between Bluetongue Virus Infections and Adaptive Immunity
Authors: Rodríguez-Martín Daniel , Louloudes-Lázaro Andrés , Avia Miguel , Martín Verónica , Rojas José M. , Sevilla Noemí
Published: August 2021

Viral infections have long provided a platform to understand the workings of immunity. For instance, great strides towards defining basic immunology concepts, such as MHC restriction of antigen presentation or T-cell memory development and maintenance, have been achieved thanks to the study of lymphocytic choriomeningitis virus (LCMV) infections. These studies have also shaped our understanding of antiviral immunity, and in particular T-cell responses. In the present review, we discuss how bluetongue virus (BTV), an economically important arbovirus from the Reoviridae family that affects ruminants, affects adaptive immunity in the natural hosts. During the initial stages of infection, BTV triggers leucopenia in the hosts. The host then mounts an adaptive immune response that controls the disease. In this work, we discuss how BTV triggers CD8+ T-cell expansion and neutralizing antibody responses, yet in some individuals viremia remains detectable after these adaptive immune mechanisms are active. We present some unpublished data showing that BTV infection also affects other T cell populations such as CD4+ T-cells or γδ T-cells, as well as B-cell numbers in the periphery. This review also discusses how BTV evades these adaptive immune mechanisms so that it can be transmitted back to the arthropod host. Understanding the interaction of BTV with immunity could ultimately define the correlates of protection with immune mechanisms that would improve our knowledge of ruminant immunology.
Challenging the Existing Model of the Hexameric HIV-1 Gag Lattice and MA Shell Superstructure: Implications for Viral Entry
Authors: Santos Joy Ramielle L. , Sun Weijie , Mangukia Tarana A. , Reyes-Serratos Eduardo , Marcet-Palacios Marcelo
Published: August 2021

Despite type 1 human immunodeficiency virus (HIV-1) being discovered in the early 1980s, significant knowledge gaps remain in our understanding of the superstructure of the HIV-1 matrix (MA) shell. Current viral assembly models assume that the MA shell originates via recruitment of group-specific antigen (Gag) polyproteins into a hexagonal lattice but fails to resolve and explain lattice overlapping that occurs when the membrane is folded into a spherical/ellipsoidal shape. It further fails to address how the shell recruits, interacts with and encompasses the viral spike envelope (Env) glycoproteins. These Env glycoproteins are crucial as they facilitate viral entry by interacting with receptors and coreceptors located on T-cells. In our previous publication, we proposed a six-lune hosohedral structure, snowflake-like model for the MA shell of HIV-1. In this article, we improve upon the six-lune hosohedral structure by incorporating into our algorithm the recruitment of complete Env glycoproteins. We generated the Env glycoprotein assembly using a combination of predetermined Env glycoprotein domains from X-ray crystallography, nuclear magnetic resonance (NMR), cryoelectron tomography, and three-dimensional prediction tools. Our novel MA shell model comprises 1028 MA trimers and 14 Env glycoproteins. Our model demonstrates the movement of Env glycoproteins in the interlunar spaces, with effective clustering at the fusion hub, where multiple Env complexes bind to T-cell receptors during the process of viral entry. Elucidating the HIV-1 MA shell structure and its interaction with the Env glycoproteins is a key step toward understanding the mechanism of HIV-1 entry.
Challenges of Rabies Serology: Defining Context of Interpretation
Authors: Moore Susan M.
Published: August 2021

The case fatality rate of rabies, nearly 100%, is one of the most unique characteristic of this ancient virus infection. The crucial role rabies virus neutralizing antibody plays in protection is both well established and explanation of why rabies serology is important. Various laboratory methods can and have been used but serum neutralization methods have long been the gold standard due to the ability to measure function (neutralization), however these methods can be difficult to perform for several reasons. Assays such as enzyme linked absorbance assays (ELISA), indirect fluorescence antibody (IFA) and more recently lateral flow methods are in use. Interpretation of results can be problematic, not only between methods but also due to modifications of the same method that can lead to misinterpretations. A common assumption in review of laboratory test results is that different methods for the same component produce comparable results under all conditions or circumstances. Assumptions and misinterpretations provide the potential for detrimental decisions, ranging from regulatory to clinically related, and most importantly what ‘level’ is protective. Review of the common challenges in performance and interpretation of rabies serology and specific examples illuminate critical issues to consider when reviewing and applying results of rabies serological testing.
Specific Recognition of a Stem-Loop RNA Structure by the Alphavirus Capsid Protein
Authors: Brown Rebecca S. , Kim Lisa , Kielian Margaret
Published: August 2021

Alphaviruses are small enveloped viruses with positive-sense RNA genomes. During infection, the alphavirus capsid protein (Cp) selectively packages and assembles with the viral genomic RNA to form the nucleocapsid core, a process critical to the production of infectious virus. Prior studies of the alphavirus Semliki Forest virus (SFV) showed that packaging and assembly are promoted by Cp binding to multiple high affinity sites on the genomic RNA. Here, we developed an in vitro Cp binding assay based on fluorescently labeled RNA oligos. We used this assay to explore the RNA sequence and structure requirements for Cp binding to site #1, the top binding site identified on the genomic RNA during all stages of virus assembly. Our results identify a stem-loop structure that promotes specific binding of the SFV Cp to site #1 RNA. This structure is also recognized by the Cps of the related alphaviruses chikungunya virus and Ross River virus.
Human Papillomavirus Related Neoplasia of the Ocular Adnexa
Authors: Ramberg Ingvild , Heegaard Steffen
Published: August 2021

Human papillomaviruses (HPV) are a large group of DNA viruses that infect the basal cells of the stratified epithelium at different anatomic locations. In the ocular adnexal region, the mucosa of the conjunctiva and the lacrimal drainage system, as well as the eyelid skin, are potential locations for HPV-related neoplasia. The role of HPV in squamous cell neoplasia of the ocular adnexa has been debated for several decades. Due to the rarity of all these tumors, large studies are not available in the scientific literature, thereby hampering the precision of the HPV prevalence estimates and the ability to conclude. Nevertheless, increasing evidence supports that defined subsets of conjunctival papillomas, intraepithelial neoplasia, and carcinomas develop in an HPV-dependent pathway. The role of HPV in squamous cell tumors arising in the lacrimal drainage system and the eyelid is still uncertain. Further, the potential of HPV status as a diagnostic, prognostic, or predictive biomarker in these diseases is a topic for future research.
Proline to Threonine Mutation at Position 162 of NS5B of Classical Swine Fever Virus Vaccine C Strain Promoted Genome Replication and Infectious Virus Production by Facilitating Initiation of RNA Synthesis
Authors: Pang Huining , Li Ling , Liu Hongru , Pan Zishu
Published: August 2021

The 3′untranslated region (3′UTR) and NS5B of classical swine fever virus (CSFV) play vital roles in viral genome replication. In this study, two chimeric viruses, vC/SM3′UTR and vC/b3′UTR, with 3′UTR substitution of CSFV Shimen strain or bovine viral diarrhea virus (BVDV) NADL strain, were constructed based on the infectious cDNA clone of CSFV vaccine C strain, respectively. After virus rescue, each recombinant chimeric virus was subjected to continuous passages in PK-15 cells. The representative passaged viruses were characterized and sequenced. Serial passages resulted in generation of mutations and the passaged viruses exhibited significantly increased genomic replication efficiency and infectious virus production compared to parent viruses. A proline to threonine mutation at position 162 of NS5B was identified in both passaged vC/SM3′UTR and vC/b3′UTR. We generated P162T mutants of two chimeras using the reverse genetics system, separately. The single P162T mutation in NS5B of vC/SM3′UTR or vC/b3′UTR played a key role in increased viral genome replication and infectious virus production. The P162T mutation increased vC/SM3′UTRP162T replication in rabbits. From RNA-dependent RNA polymerase (RdRp) assays in vitro, the NS5B containing P162T mutation (NS5BP162T) exhibited enhanced RdRp activity for different RNA templates. We further identified that the enhanced RdRp activity originated from increased initiation efficiency of RNA synthesis. These findings revealed a novel function for the NS5B residue 162 in modulating pestivirus replication.
Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic
Authors: Castañeda Sergio , Patiño Luz H. , Muñoz Marina , Ballesteros Nathalia , Guerrero-Araya Enzo , Paredes-Sabja Daniel , Flórez Carolina , Gomez Sergio , Ramírez-Santana Carolina , Salguero Gustavo , Gallo Juan E. , Paniz-Mondolfi Alberto E. , Ramírez Juan David
Published: August 2021

Current efforts to understand the epidemiology, transmission dynamics and emergence of novel SARS-CoV-2 variants worldwide has enabled the scientific community to generate critical information aimed at implementing disease surveillance and control measures, as well as to reduce the social, economic and health impact of the pandemic. Herein, we applied an epidemic model coupled with genomic analysis to assess the SARS-CoV-2 transmission dynamics in Colombia. This epidemic model allowed to identify the geographical distribution, Rt dynamics and predict the course of the pandemic considering current implementation of countermeasures. The analysis of the incidence rate per 100,000 inhabitants carried out across different regions of Colombia allowed visualizing the changes in the geographic distribution of cases. The cumulative incidence during the timeframe March 2020 to March 2021 revealed that Bogotá (8063.0), Quindío (5482.71), Amazonas (5055.68), Antioquia (4922.35) and Tolima (4724.41) were the departments with the highest incidence rate. The highest median Rt during the first period evaluated was 2.13 and 1.09 in the second period; with this model, we identified improving opportunities in health decision making related to controlling the pandemic, diagnostic testing capacity, case registration and reporting, among others. Genomic analysis revealed 52 circulating SARS-CoV-2 lineages in Colombia detected from 774 genomes sequenced throughout the first year of the pandemic. The genomes grouped into four main clusters and exhibited 19 polymorphisms. Our results provide essential information on the spread of the pandemic countrywide despite implementation of early containment measures. In addition, we aim to provide deeper phylogenetic insights to better understand the evolution of SARS-CoV-2 in light of the latent emergence of novel variants and how these may potentially influence transmissibility and infectivity.