bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Potential of Preprints in Geochemistry: The Good, the Bad, and the Ugly
Authors: Pourret Olivier , Irawan Dasapta , Tennant Jonathan
Published: April 2020

In recent years, the pace of the dissemination of scientific information has increased. In this context, the possibility and value of sharing open access (OA) online manuscripts in their preprint form seem to be growing in many scientific fields. More and more platforms are especially dedicated to free preprint publishing. They are published, non-peer-reviewed scholarly papers that typically precede publication in a peer-reviewed journal. They have been a part of science since at least the 1960s. In 1990, Tim Berners-Lee created the World Wide Web to help researchers share knowledge easily. A few months later, in August 1991, as a centralized web-based network, arXiv was created. arXiv is arguably the most influential preprint platform and has supported the fields of physics, mathematics and computer science for over 30 years. Since, preprint platforms have become popular in many disciplines (e.g., bioRxiv for biological sciences) due to the increasing drive towards OA publishing, and can be publisher- or community-driven, profit or not for profit, and based on proprietary or free and open source software. A range of discipline-specific or cross-domain platforms now exist, with exponential growth these last five years. While preprints as a whole still represent only a small proportion of scholarly publishing, a strong community of early adopters is already beginning to experiment with such value-enhancing tools in many more disciplines than before. The two main options for geochemists are EarthArXiv and ESSOAr. A “one size fits all” model for preprints would never work across the entire scientific community. The geochemistry community needs to develop and sustain their own model.
The Assessment of Climate Change on Rainfall-Runoff Erosivity in the Chirchik–Akhangaran Basin, Uzbekistan
Authors: Gafforov Khusen Sh. , Bao Anming , Rakhimov Shavkat , Liu Tie , Abdullaev Farkhod , Jiang Liangliang , Durdiev Khaydar , Duulatov Eldiiar , Rakhimova Moldir , Mukanov Yerbolat
Published: April 2020

Changes in the frequency or intensity of rainfall due to climate always affect the conservation of soil resources, which leads to land degradation. The importance of assessing past and future climate differences plays an important role in future planning in relation to climate change. The spatiotemporal variability of erosivity depending on precipitation using the rainfall erosivity (R) of Universal Soil Loss Equation under the global circulation model (GCM) scenarios in the Chirchik–Akhangaran Basin (CHAB), which is in the northeastern part of the Republic of Uzbekistan, was statistically downscaled by using the delta method in Representative Concentration Pathways (RCPs) 4.5 and 8.5 during the periods of the 2030s, 2050s and 2070s. The (R) was used to determine the erosivity of precipitation, and the Revised Universal Soil Loss Equation (RUSLE) itself determined the effects of changes in erosivity. Ten weather station observational data points for the period from 1990 to 2016 were used to validate the global circulation models (GCMs) and erosion model. The assessment results showed an increase in precipitation from the baseline by an average of 11.8%, 14.1% and 16.3% for all models by 2030, 2050 and 2070, respectively, while at the same time, soil loss increased in parallel with precipitation by 17.1%, 20.5 % and 23.3%, respectively, in certain scenarios. The highest rainfall was observed for the models ACCESS1–3 and CanESM2 on both RCPs and periods, while more intense rainfall was the main reason for the increase in the spatial and temporal erosion activity of the rainfall-runoff. This study is a useful reference for improving soil conservation, preventing water erosion and ensuring the future sustainability of agricultural products, as well as improving the operational management and planning of agriculture.
Ni-Doped Titanium Dioxide Films Obtained by Plasma Electrolytic Oxidation in Refrigerated Electrolytes
Authors: Arab Hamed , Chiarello Gian Luca , Selli Elena , Bomboi Giacomo , Calloni Alberto , Bussetti Gianlorenzo , Albani Guglielmo , Bestetti Massimiliano , Franz Silvia
Published: April 2020

Porous crystalline Ni-doped TiO2 films were produced using DC plasma electrolytic oxidation in refrigerated H2SO4 aqueous solutions containing NiSO4. The crystalline phase structure consisted of a mixture of anatase and rutile, ranging from ~30 to ~80 wt % rutile. The oxide films obtained at low NiSO4 concentration showed the highest photocurrent values under monochromatic irradiation in the UV-vis range, outperforming pure TiO2. By increasing NiSO4 concentration above a threshold value, the photoelectrochemical activity of the films decreased below that of undoped TiO2. Similar results were obtained using cyclic voltammetry upon polychromatic UV-vis irradiation. Glow discharge optical emission spectrometry (GD-OES) analysis evidenced a sulfur signal peaking at the TiO2/Ti interface. XPS spectra revealed that oxidized Ni2+, S4+ and S6+ ions were included in the oxide films. In agreement with photocurrent measurements, photoluminescence (PL) spectra confirmed that less intense PL emission, i.e., a lower electron-hole recombination rate, was observed for Ni-doped samples, though overdoping was detrimental.
The Immobilization of Oxindole Derivatives Using New Designed Functionalized C60 Nanomolecules
Authors: Czeleń Przemysław , Szefler Beata
Published: April 2020

Indirubin and its analogs such as oxindole derivatives are well known as competitive inhibitors of cyclin-dependent kinase 2 (CDK2) and play an important role in the creation of therapies in many cancer diseases. Recent research, in order to increase efficiency, is aimed at creating targeted therapy, which is often based on the immobilization of drugs on the surface of nanocarriers. In this work, two oxindole derivatives were used to test the binding capabilities of newly in silico designed C60 fullerene derivatives. Seventy functionalized nanostructures were created by the addition of amino acid substituents to the single phenyl ring attached to the fullerene surface. Realized calculations, based on flexible docking methods, allowed for obtaining energetic characteristics and structural aspects of complexes created by nanomolecules with considered ligands. Analysis of obtained complexes shows that symmetric substitution to position R3 and R5 allows obtaining fullerene derivatives exhibiting the highest binding capabilities, while the lowest ones are the effect of asymmetric substitution (R2; R4). Obtained values clearly allowed to select a group of substituents and substitution sites that provide the most stable complexes which can be used to create new nanocarriers for the group of drugs under consideration.
Symmetrical Noncovalent Interactions Br···Br Observed in Crystal Structure of Exotic Primary Peroxide
Authors: Bolotin Dmitrii S. , Il’in Mikhail V. , Suslonov Vitalii V. , Novikov Alexander S.
Published: April 2020

4-Bromobenzamidrazone reacts with cyclopentanone giving 3-(4-bromophenyl)-5-(4-peroxobutyl)-1,2,4-triazole, which precipitated as pale-yellow crystals during the reaction. The intermolecular noncovalent interactions Br···Br in the single-crystal XRD structure of the peroxo compound were studied theoretically using quantum chemical calculations (ωB97XD/x2c-TZVPPall) and quantum theory of atoms in molecules (QTAIM) analysis. These attractive intermolecular noncovalent interactions Br···Br is type I halogen···halogen contacts and their estimated energy is 2.2–2.5 kcal/mol. These weak interactions are suggested to be one of the driving forces (albeit surely not the main one) for crystallization of the peroxo compound during the reaction and thus its stabilization in the solid state.
Microstructure Instance Segmentation from Aluminum Alloy Metallographic Image Using Different Loss Functions
Authors: Chen Dali , Guo Dinghao , Liu Shixin , Liu Fang
Published: April 2020

Automatic segmentation of metallographic image is very important for the implementation of an automatic metallographic analysis system. In this paper, a novel instance segmentation framework of a metallographic image was implemented, which can assign each pixel to a physical instance of a microstructure. In this framework, we used the Mask R-CNN as the basic network to complete the learning and recognition of the latent feature of an aluminum alloy microstructure. Meanwhile, we implemented five different loss functions based on this framework and compared the influence of these loss functions on metallographic image segmentation performance. We carried out several experiments to verify the effectiveness of the proposed framework. In these experiments, we compared and analyzed six different evaluation metrics and provided constructive suggestions for the performance evaluation of metallographic image segmentation method. A large number of experimental results have shown that the proposed method can achieve the instance segmentation of an aluminum alloy metallographic image and the segmentation results are satisfactory.
Protein Interaction with Dendrimer Monolayers: Energy and Surface Topology
Authors: Lungu Claudiu N. , Füstös Melinda E. , Grudziński Ireneusz P. , Olteanu Gabriel , Putz Mihai V.
Published: April 2020

Protein interaction with polymers layers is a keystone in designing bio-nano devices. Polyamidoamines (PAMAMs) are well-known polymers. Zero aromatic core dendrimers (ZAC) are molecules with no proven toxic effect in cultured cells. When coating nanodevices with enzymatic systems, active sites are disturbed by an interaction with the biosystem surface. Computational methods were used in order to simulate, characterize, and quantify protein–polymer interaction. Protein corona, i.e., surface proteins disposed on a viral membrane or nanodevice outer surface, are crucial in interactions with a potential pharmacological target or receptor. Corona symmetry has been observed in the Middle East respiratory syndrome-related coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a protein alpha 1 antitrypsin’s a crystallographic structure was chosen. Protein–mono dendrimer layer systems were generated using in silico methods in order to simulate their interaction. Interactions were quantified using topological and quantum mechanical strategies. Results showed that PAMAM and ZAC interact differently with alpha 1 antitrypsin. Energy and topological surfaces of protein vary accordingly with the dendrimer monolayer. Topological surfaces have a higher sensibility in describing the interactions.
An Ontology Based on the Timeline of Log2timeline and Psort Using Abstraction Approach in Digital Forensics
Authors: Bhandari Sandeepak , Jusas Vacius
Published: April 2020

Digital forensics practitioners encounter numerous new terminologies during time-intensive digital investigation processes because of the explosive growth of the web, an immense amount of data, and rapid changes in technology. In such a scenario, the time needed to find and interpret the cause of the potential digital incident can be affected by the complexity involved in understanding the meaning of newly encountered terminologies. Although various approaches have been designed to assist digital practitioners in understanding the newly encountered terminologies during the investigation of the accident, none of them is capable of supporting investigators to interpret new terminologies. Our work focuses on reconstructing and analyzing the timeline of events and artifacts backed by the abstraction concept to help practitioners in reasoning about the perceived meaning of different digital forensics terminologies that are encountered during the investigation. This paper introduces an ontological approach based on the abstraction concept to reconstruct the timeline provided by command-based digital forensic tools, i.e., Log2timeline and Psort in the L2TCSV format, and assist in resolving the meaning of new encountered concepts. The performed experiments show that the novel methodology is capable of enhancing the timeline and assisting practitioners in determining the significance of encountered terminologies or concepts.
New Exact Solutions of the Conformable Space-Time Sharma–Tasso–Olver Equation Using Two Reliable Methods
Authors: Sirisubtawee Sekson , Koonprasert Sanoe , Sungnul Surattana
Published: April 2020

The major purpose of this article is to seek for exact traveling wave solutions of the nonlinear space-time Sharma–Tasso–Olver equation in the sense of conformable derivatives. The novel ( G ′ G ) -expansion method and the generalized Kudryashov method, which are analytical, powerful, and reliable methods, are used to solve the equation via a fractional complex transformation. The exact solutions of the equation, obtained using the novel ( G ′ G ) -expansion method, can be classified in terms of hyperbolic, trigonometric, and rational function solutions. Applying the generalized Kudryashov method to the equation, we obtain explicit exact solutions expressed as fractional solutions of the exponential functions. The exact solutions obtained using the two methods represent some physical behaviors such as a singularly periodic traveling wave solution and a singular multiple-soliton solution. Some selected solutions of the equation are graphically portrayed including 3-D, 2-D, and contour plots. As a result, some innovative exact solutions of the equation are produced via the methods, and they are not the same as the ones obtained using other techniques utilized previously.
Research of Wireless Congestion Control Algorithm Based on EKF
Authors: Wang Hui , Tang Junyong , Hong Bo
Published: April 2020

The random variation of bandwidth in wireless networks causes some significant challenges to the congestion control protocols based on bandwidth estimation. In this paper, a wireless congestion control scheme based on extended Kalman filtering and bandwidth (CSEKB) is proposed. The CSEKB can effectively perceive the bandwidth oscillation of wireless networks and distinguish the type of packet loss by establishing a noise perception factor. According to the congestion factor, the congestion control parameters are adjusted to correspondingly improve the performance of the wireless network. Moreover, the variation trend of the size of the congestion window presents a law of similar normal distribution curve, which has a certain degree of local symmetry. The CSEKB was implemented in Network simulator 3 (NS3) and compared with TCP Westwood (TCPW), CUBIC, and extended Kalman filtering-based bandwidth estimation (EBE). Through extensive simulation studies, the proposed CSEKB demonstrated the significant performance in wireless networks. First, the CSEKB can achieve congestion control based on the accurate prediction of available bandwidth, and improve average throughput and link utilization. In addition, the CSEKB has good fairness and friendliness compared with several other well-known congestion control methods.
Entropy Generation and Consequences of MHD in Darcy–Forchheimer Nanofluid Flow Bounded by Non-Linearly Stretching Surface
Authors: Rasool Ghulam , Shafiq Anum , Khan Ilyas , Baleanu Dumitru , Sooppy Nisar Kottakkaran , Shahzadi Gullnaz
Published: April 2020

Present communication aims to inspect the entropy optimization, heat and mass transport in Darcy-Forchheimer nanofluid flow surrounded by a non-linearly stretching surface. Navier-Stokes model based governing equations for non-Newtonian nanofluids having symmetric components in various terms are considered. Non-linear stretching is assumed to be the driving force whereas influence of thermal radiation, Brownian diffusion, dissipation and thermophoresis is considered. Importantly, entropy optimization is performed using second law of thermodynamics. Governing problems are converted into nonlinear ordinary problems (ODEs) using suitably adjusted transformations. RK-45 based built-in shooting mechanism is used to solve the problems. Final outcomes are plotted graphically. In addition to velocity, temperature, concentration and Bejan number, the stream lines, contour graphs and density graphs have been prepared. For their industrial and engineering importance, results for wall-drag force, heat flux (Nusselt) rate and mass flux (Sherwood) rate are also given in tabular data form. Outputs indicate that velocity reduces for Forchheimer number as well as for the porosity factor. However, a rise is noted in temperature distribution for elevated values of thermal radiation. Entropy optimization shows enhancement for larger values of temperature difference ratio. Skin-friction enhances for all relevant parameters involved in momentum equation.
A Method for Measuring Systems Thinking Learning
Authors: Taylor Seth , Calvo-Amodio Javier , Well Jay
Published: April 2020

The myriad of problems facing the world today are increasingly complex, dynamic, and transcend multiple domains. This necessitates the need for trans-disciplinary approaches capable of providing a framework to help solve these problems. Systems thinking provides the skills necessary for people to approach these types of problems. However, a lack of awareness and understanding of systems thinking hinders a potential systems-literate and systems-capable society. Systems thinking is comprised of four underlying concepts or skills: distinction-making, organizing systems, inter-relating, and perspective-taking. The path to becoming a systems thinker follows a process comprised of three levels—sensibility (awareness of systems), literacy (knowledge of systems), and capability (understanding of systems)—repeated across multiple learning phases. During this research study, a method was defined to measure whether non-experts learned the underlying systems thinking concepts according to this learning process. An experiment was conducted with 97 middle and high school students who were asked to draw a fish-tank system before and after being taught to apply the systems thinking concepts as skills for identifying elements, interactions, and roles/purposes. The results provide evidence to conclude that student learning of systems thinking significantly increased from the first drawing to the second drawing.
Genotoxic Effects of Aluminum Chloride and Their Relationship with N-Nitroso-N-Methylurea (NMU)-Induced Breast Cancer in Sprague Dawley Rats
Authors: García-Alegría Alejandro Monserrat , Gómez-Álvarez Agustín , Anduro-Corona Iván , Burgos-Hernández Armando , Ruíz-Bustos Eduardo , Canett-Romero Rafael , González-Ríos Humberto , López-Cervantes José Guillermo , Rodríguez-Martínez Karen Lillian , Astiazaran-Garcia Humberto
Published: April 2020

Recently, soluble forms of aluminum for human use or consumption have been determined to be potentially toxic due to their association with hepatic, neurological, hematological, neoplastic, and bone conditions. This study aims to assess the genotoxic effect of aluminum chloride on genomic instability associated with the onset of N-nitroso-N-methylurea (NMU)-induced breast cancer in Sprague Dawley rats. The dietary behavior of the rats was assessed, and the concentration of aluminum in the mammary glands was determined using atomic absorption spectroscopy. Genomic instability was determined in the histological sections of mammary glands stained with hematoxylin and eosin. Moreover, micronucleus in peripheral blood and comet assays were performed. The results of dietary behavior evaluation indicated no significant differences between the experimental treatments. However, aluminum concentration in breast tissues was high in the +2000Al/−NMU treatment. This experimental treatment caused moderate intraductal cell proliferation, lymph node hyperplasia, and serous gland adenoma. Furthermore, micronucleus and comet test results revealed that +2000Al/−NMU led to a genotoxic effect after a 10-day exposure and the damage was more evident after a 15-day exposure. Therefore, in conclusion, genomic instability is present and the experimental conditions assessed are not associated with breast cancer.
Defensive Venoms: Is Pain Sufficient for Predator Deterrence?
Authors: Niermann Crystal N. , Tate Travis G. , Suto Amber L. , Barajas Rolando , White Hope A. , Guswiler Olivia D. , Secor Stephen M. , Rowe Ashlee H. , Rowe Matthew P.
Published: April 2020

Pain, though unpleasant, is adaptive in calling an animal’s attention to potential tissue damage. A long list of animals representing diverse taxa possess venom-mediated, pain-inducing bites or stings that work by co-opting the pain-sensing pathways of potential enemies. Typically, such venoms include toxins that cause tissue damage or disrupt neuronal activity, rendering painful stings honest indicators of harm. But could pain alone be sufficient for deterring a hungry predator? Some venomologists have argued “no”; predators, in the absence of injury, would “see through” the bluff of a painful but otherwise benign sting or bite. Because most algogenic venoms are also toxic (although not vice versa), it has been difficult to disentangle the relative contributions of each component to predator deterrence. Southern grasshopper mice (Onychomys torridus) are voracious predators of arthropods, feeding on a diversity of scorpion species whose stings vary in painfulness, including painful Arizona bark scorpions (Centruroides sculpturatus) and essentially painless stripe-tailed scorpions (Paravaejovis spinigerus). Moreover, southern grasshopper mice have evolved resistance to the lethal toxins in bark scorpion venom, rendering a sting from these scorpions painful but harmless. Results from a series of laboratory experiments demonstrate that painful stings matter. Grasshopper mice preferred to prey on stripe-tailed scorpions rather than bark scorpions when both species could sting; the preference disappeared when each species had their stingers blocked. A painful sting therefore appears necessary for a scorpion to deter a hungry grasshopper mouse, but it may not always be sufficient: after first attacking and consuming a painless stripe-tailed scorpion, many grasshopper mice went on to attack, kill, and eat a bark scorpion even when the scorpion was capable of stinging. Defensive venoms that result in tissue damage or neurological dysfunction may, thus, be required to condition greater aversion than venoms causing pain alone.
Enzymatic Synthesis of Modified Alternaria Mycotoxins Using a Whole-Cell Biotransformation System
Authors: Scheibenzuber Sophie , Hoffmann Thomas , Effenberger Isabelle , Schwab Wilfried , Asam Stefan , Rychlik Michael
Published: April 2020

Reference standards for Alternaria mycotoxins are rarely available, especially the modified mycotoxins alternariol-3-glucoside (AOH-3-G), alternariol-9-glucoside (AOH-9-G), and alternariol monomethylether-3-glucoside (AME-3-G). To obtain these three glucosides as analytical standards for method development and method validation, alternariol and alternariol monomethylether were enzymatically glycosylated in a whole-cell biotransformation system using a glycosyltransferase from strawberry (Fragaria x ananassa), namely UGT71A44, expressed in Escherichia coli (E. coli). The formed glucosides were isolated, purified, and structurally characterized. The exact amount of the isolated compounds was determined using high-performance liquid chromatography with UV-detection (HPLC-UV) and quantitative nuclear resonance spectroscopy (qNMR). This method has proved to be highly effective with biotransformation rates of 58% for AOH-3-G, 5% for AOH-9-G, and 24% for AME-3-G.
Enzyme Immunoassay for Measuring Aflatoxin B1 in Legal Cannabis
Authors: Di Nardo Fabio , Cavalera Simone , Baggiani Claudio , Chiarello Matteo , Pazzi Marco , Anfossi Laura
Published: April 2020

The diffusion of the legalization of cannabis for recreational, medicinal and nutraceutical uses requires the development of adequate analytical methods to assure the safety and security of such products. In particular, aflatoxins are considered to pose a major risk for the health of cannabis consumers. Among analytical methods that allows for adequate monitoring of food safety, immunoassays play a major role thanks to their cost-effectiveness, high-throughput capacity, simplicity and limited requirement for equipment and skilled operators. Therefore, a rapid and sensitive enzyme immunoassay has been adapted to measure the most hazardous aflatoxin B1 in cannabis products. The assay was acceptably accurate (recovery rate: 78–136%), reproducible (intra- and inter-assay means coefficients of variation 11.8% and 13.8%, respectively), and sensitive (limit of detection and range of quantification: 0.35 ng mL−1 and 0.4–2 ng mL−1, respectively corresponding to 7 ng g−1 and 8–40 ng g−1 ng g−1 in the plant) and provided results which agreed with a HPLC-MS/MS method for the direct analysis of aflatoxin B1 in cannabis inflorescence and leaves. In addition, the carcinogenic aflatoxin B1 was detected in 50% of the cannabis products analyzed (14 samples collected from small retails) at levels exceeding those admitted by the European Union in commodities intended for direct human consumption, thus envisaging the need for effective surveillance of aflatoxin contamination in legal cannabis.
Orthohantavirus Isolated in Reservoir Host Cells Displays Minimal Genetic Changes and Retains Wild-Type Infection Properties
Authors: Strandin Tomas , Smura Teemu , Ahola Paula , Aaltonen Kirsi , Sironen Tarja , Hepojoki Jussi , Eckerle Isabella , Ulrich Rainer G. , Vapalahti Olli , Kipar Anja , Forbes Kristian M.
Published: April 2020

Orthohantaviruses are globally emerging zoonotic pathogens. While the reservoir host role of several rodent species is well-established, detailed research on the mechanisms of host-othohantavirus interactions has been constrained by the lack of an experimental system that is able to effectively replicate natural infections in controlled settings. Here we report the isolation, and genetic and phenotypic characterization of a novel Puumala orthohantavirus (PUUV) in cells derived from its reservoir host, the bank vole. The isolation process resulted in cell culture infection that evaded antiviral responses, persisted cell passaging, and had minor viral genome alterations. Critically, experimental infections of bank voles with the new isolate resembled natural infections in terms of viral load and host cell distribution. When compared to an attenuated Vero E6 cell-adapted PUUV Kazan strain, the novel isolate demonstrated delayed virus-specific humoral responses. A lack of virus-specific antibodies was also observed during experimental infections with wild-type PUUV, suggesting that delayed seroconversion could be a general phenomenon during orthohantavirus infection in reservoir hosts. Our results demonstrate that orthohantavirus isolation on cells derived from a vole reservoir host retains wild-type infection properties and should be considered the method of choice for experimental infection models to replicate natural processes.
Human West Nile Virus Lineage 2 Infection: Epidemiological, Clinical, and Virological Findings
Authors: Pacenti Monia , Sinigaglia Alessandro , Franchin Elisa , Pagni Silvana , Lavezzo Enrico , Montarsi Fabrizio , Capelli Gioia , Barzon Luisa
Published: April 2020

West Nile virus (WNV) lineage 2 is expanding and causing large outbreaks in Europe. In this study, we analyzed the epidemiological, clinical, and virological features of WNV lineage 2 infection during the large outbreak that occurred in northern Italy in 2018. The study population included 86 patients with neuroinvasive disease (WNND), 307 with fever (WNF), and 34 blood donors. Phylogenetic analysis of WNV full genome sequences from patients’ samples showed that the virus belonged to the widespread central/southern European clade of WNV lineage 2 and was circulating in the area at least since 2014. The incidence of WNND and WNF progressively increased with age and was higher in males than in females. Among WNND patients, the case fatality rate was 22%. About 70% of blood donors reported symptoms during follow-up. Within the first week after symptom onset, WNV RNA was detectable in the blood or urine of 80% of patients, while 20% and 40% of WNND and WNF patients, respectively, were WNV IgM-seronegative. In CSF samples of WNND patients, WNV RNA was typically detectable when WNV IgM antibodies were absent. Blunted or no WNV IgM response and high WNV IgG levels were observed in seven patients with previous flavivirus immunity.
The Nef Protein of the Macrophage Tropic HIV-1 Strain AD8 Counteracts Human BST-2/Tetherin
Authors: Giese Sebastian , Lawrence Scott P. , Mazzon Michela , Nijmeijer Bernadien M. , Marsh Mark
Published: April 2020

Bone Marrow Stromal Cell Antigen 2 (BST-2)/tetherin inhibits the release of numerous enveloped viruses by physically tethering nascent particles to infected cells during the process of viral budding from the cell surface. Tetherin also restricts human immunodeficiency virus (HIV), and pandemic main (M) group HIV type 1s (HIV-1s) are thought to rely exclusively on their Vpu proteins to overcome tetherin-mediated restriction of virus release. However, at least one M group HIV-1 strain, the macrophage-tropic primary AD8 isolate, is unable to express Vpu due to a mutation in its translation initiation codon. Here, using primary monocyte-derived macrophages (MDMs), we show that AD8 Nef protein can compensate for the absence of Vpu and restore virus release to wild type levels. We demonstrate that HIV-1 AD8 Nef reduces endogenous cell surface tetherin levels, physically separating it from the site of viral budding, thus preventing HIV retention. Mechanistically, AD8 Nef enhances internalisation of the long isoform of human tetherin, leading to perinuclear accumulation of the restriction factor. Finally, we show that Nef proteins from other HIV strains also display varying degrees of tetherin antagonism. Overall, we show that M group HIV-1s can use an accessory protein other than Vpu to antagonise human tetherin.
Survival of Human Norovirus Surrogates in Water upon Exposure to Thermal and Non-Thermal Antiviral Treatments
Authors: Zhu Shu , Barnes Candace , Bhar Sutonuka , Hoyeck Papa , Galbraith Annalise N. , Devabhaktuni Divya , Karst Stephanie M. , Montazeri Naim , Jones Melissa K.
Published: April 2020

Human noroviruses are the leading cause of foodborne gastroenteritis worldwide and disease outbreaks have been linked to contaminated surface waters as well as to produce consumption. Noroviruses are extremely stable in water and their presence is being detected with increasing frequency, yet there are no viable methods for reducing norovirus contamination in environmental water. Despite this, there is little knowledge regarding the physical and chemical factors that influence the environmental persistence of this pathogen. This study evaluated the impact of common chemical and physical properties of surface water on the stability of murine norovirus and examined the effect of food-safe chitosan microparticles on infectivity of two human norovirus surrogates. While chemical additives had a minor impact on virus survival, chitosan microparticles significantly reduced infectious titers of both murine norovirus and MS2 bacteriophage.
Proteomic and Bioinformatic Analysis of Streptococcus suis Human Isolates: Combined Prediction of Potential Vaccine Candidates
Authors: Prados de la Torre Esther , Rodríguez-Franco Antonio , Rodríguez-Ortega Manuel J.
Published: April 2020

Streptococcus suis is a Gram-positive bacterium responsible for major infections in pigs and economic losses in the livestock industry, but also an emerging zoonotic pathogen causing serious diseases in humans. No vaccine is available so far against this microorganism. Conserved surface proteins are among the most promising candidates for new and effective vaccines. Until now, research on this pathogen has focused on swine isolates, but there is a lack of studies to identify and characterize surface proteins from human clinical isolates. In this work, we performed a comparative proteomic analysis of six clinical isolates from human patients, all belonging to the major serotype 2, by “shaving” the live bacterial cells with trypsin, followed by LC-MS/MS analysis. We identified 131 predicted surface proteins and carried out a label-free semi-quantitative analysis of protein abundances within the six strains. Then, we combined our proteomics results with bioinformatic tools to help improving the selection of novel antigens that can enter the pipeline of vaccine candidate testing. Our work is then a complement to the reverse vaccinology concept.
Plant-Produced N-glycosylated Ag85A Exhibits Enhanced Vaccine Efficacy Against Mycobacterium tuberculosis HN878 Through Balanced Multifunctional Th1 T Cell Immunity
Authors: Kim Hongmin , Kwon Kee Woong , Park Jaehun , Kang Hyangju , Lee Yongjik , Sohn Eun-Ju , Hwang Inhwan , Eum Seok-Yong , Shin Sung Jae
Published: April 2020

Tuberculosis (TB) is one of the deadliest infectious diseases worldwide and is caused by Mycobacterium tuberculosis (Mtb). An effective vaccine to prevent TB is considered the most cost-effective measure for controlling this disease. Many different vaccine antigen (Ag) candidates, including well-known and newly identified Ags, have been evaluated in clinical and preclinical studies. In this study, we took advantage of a plant system of protein expression using Nicotiana benthamiana to produce N-glycosylated antigen 85A (G-Ag85A), which is one of the most well-characterized vaccine Ag candidates in the field of TB vaccines, and compared its immunogenicity and vaccine efficacy with those of nonglycosylated Ag85A (NG-Ag85A) produced with an Escherichia coli system. Notably, G-Ag85A induced a more robust IFN-γ response than NG-Ag85A, which indicated that G-Ag85A is well recognized by the host immune system during Mtb infection. We subsequently compared the vaccine potential of G-Ag85A and NG-Ag85A by evaluating their immunological features and substantial protection efficacies. Interestingly, G-Ag85A yielded moderately enhanced long-term protective efficacy, as measured in terms of bacterial burden and lung inflammation. Strikingly, G-Ag85A-immunized mice showed a more balanced proportion of multifunctional Th1-biased immune responses with sustained IFN-γ response than did NG-Ag85A-immunized mice. Collectively, plant-derived G-Ag85A could induce protective and balanced Th1 responses and confer long-term protection against a hypervirulent Mtb Beijing strain infection, which indicated that plant-produced G-Ag85A might provide an excellent example for the production of an Mtb subunit vaccine Ag and could be an effective platform for the development of anti-TB vaccines.
Protective Malaria Vaccine in Mice Based on the Plasmodium vivax Circumsporozoite Protein Fused with the Mumps Nucleocapsid Protein
Authors: Marques Rodolfo F. , Gimenez Alba Marina , Aliprandini Eduardo , Novais Janaina T. , Cury Diego P. , Watanabe Ii-Sei , Dominguez Mariana R. , Silveira Eduardo L. V. , Amino Rogerio , Soares Irene S.
Published: April 2020

Plasmodium vivax is the most common species of human malaria parasite found outside Africa, with high endemicity in Asia, Central and South America, and Oceania. Although Plasmodium falciparum causes the majority of deaths, P. vivax can lead to severe malaria and result in significant morbidity and mortality. The development of a protective vaccine will be a major step toward malaria elimination. Recently, a formulation containing the three allelic variants of the P. vivax circumsporozoite protein (PvCSP—All epitopes) showed partial protection in mice after a challenge with the hybrid Plasmodium berghei (Pb) sporozoite, in which the PbCSP central repeats were replaced by the VK210 PvCSP repeats (Pb/Pv sporozoite). In the present study, the chimeric PvCSP allelic variants (VK210, VK247, and P. vivax-like) were fused with the mumps virus nucleocapsid protein in the absence (NLP-CSPR) or presence of the conserved C-terminal (CT) domain of PvCSP (NLP-CSPCT). To elicit stronger humoral and cellular responses, Pichia pastoris yeast was used to assemble them as nucleocapsid-like particles (NLPs). Mice were immunized with each recombinant protein adjuvanted with Poly (I:C) and presented a high frequency of antigen-specific antibody-secreting cells (ASCs) on days 5 and 30, respectively, in the spleen and bone marrow. Moreover, high IgG titers against all PvCSP variants were detected in the sera. Later, these immunized mice with NLP-CSPCT were challenged with Pb/Pv sporozoites. Sterile protection was observed in 30% of the challenged mice. Therefore, this vaccine formulation use has the potential to be a good candidate for the development of a universal vaccine against P. vivax malaria.
The Impact of Locoregional Treatment on Response to Nivolumab in Advanced Platinum Refractory Head and Neck Cancer: The Need Trial
Authors: Botticelli Andrea , Mezi Silvia , Pomati Giulia , Sciattella Paolo , Cerbelli Bruna , Roberto Michela , Mammone Giulia , Cirillo Alessio , Cassano Alessandra , Di Dio Carmela , Cortellini Alessio , Pizzuti Laura , Ronzino Graziana , Salati Massimiliano , Vici Patrizia , Polimeni Antonella , Merlano Marco Carlo , Nuti Marianna , Marchetti Paolo
Published: April 2020

Background: Previous locoregional treatment could affect the response to nivolumab in platinum-refractory recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC). The aim of this study is to evaluate the impact of the clinicopathological characteristics and previous treatment in predicting early progression to nivolumab in a real-world population. Methods: This is an observational, multicenter retrospective/prospective study including patients (pts) with platinum refractory R/M HNSCC who received nivolumab 240 mg every 2 weeks from October 2018 to October 2019. We analyzed the association between previous treatment, clinicopathological characteristics, and early progression (within 3 months). Results: Data from 61 pts were reviewed. Median age was 67 years (30–82). Forty-two pts (69%) received previous locoregional treatment. Early progression to nivolumab occurred in 36 pts (59%), while clinical benefit (stable disease and partial response) was achieved in 25 pts (41%). Early progression to nivolumab was significantly associated to previous locoregional treatment both at univariate and multivariate analysis (p = 0.005 and p = 0.048, respectively). Conclusion: nivolumab in R/M HNSCC is burdened with a high early progression rate. Previous wide neck dissection and high dose radiotherapy may compromise the efficacy of nivolumab, distorting the anatomy of the local lymphatic system and hindering the priming of immune response.
Wildfire Effects on Groundwater Quality from Springs Connected to Small Public Supply Systems in a Peri-Urban Forest Area (Braga Region, NW Portugal)
Authors: Mansilha Catarina , Melo Armindo , Martins Zita E. , Ferreira Isabel M. P. L. V. O. , Pereira Ana Maria , Espinha Marques Jorge
Published: April 2020

Peri-urban areas are territories that combine urban and rural features, being particularly vulnerable to wildfire due to the contact between human infrastructures and dense vegetation. Wildfires may cause considerable direct and indirect effects on the local water cycle, but the influence on groundwater quality is still poorly understood. The aim of this study was to characterize the chemistry of several springs connected to small public supply systems in a peri-urban area, following a large wildfire that took place in October 2017. Groundwater samples were collected in four springs that emerged within burned forests, while control samples were from one spring located in an unburned area. Sampling took place from October 2017 until September 2018, starting 15 days after the wildfire occurrence, to evaluate the influence of the time after fire and the effect of precipitation events on groundwater composition. Groundwater samples collected in burned areas presented increased content of sulfate, fluoride and nitrogen and variability in pH values. Iron, manganese and chromium contents also increased during the sampling period. Post-fire concentrations of polycyclic aromatic hydrocarbons (PAHs), mainly the carcinogenic ones, increased especially after intense winter and spring rain events, but the levels did not exceed the guideline values for drinking water.
Simulation of a Water Distribution Network with Key Performance Indicators for Spatio-Temporal Analysis and Operation of Highly Stressed Water Infrastructure
Authors: Kofinas Dimitris , Ulanczyk Rafal , Laspidou Chrysi S.
Published: April 2020

An annual and lumped water balance assessment of a water distribution network is recommended by the International Water Association as a first step and prerequisite for improving the performance of the network by minimizing real/physical water losses, burst incidents, water theft, nonrevenue water, and energy consumption, among others. The current work suggests a modeling approach for developing the water balance of a network spatio-temporarily, in hour time-scale and neighborhood granularity. It exploits already established key performance indicators and introduces some new ones to highlight the potential in improving the management of a water distribution network when having a detailed spatio-temporal supervision, especially when the spatial and temporal conditions are variable. The methodology is applied in a seasonally touristic and hilly case study. Additionally, a pressure management scheme is applied to further exploit the potential of such a toolkit. For the investigated case study, the town of Skiathos, the annual real losses are estimated equal to 50.9–52.2% of the system input volume, while apparent losses are estimated to be about 5.6–6.6%. Losses depict intense seasonal variability. Real losses range from 38.8–39.6% in summer months to 63.3–64.7% in winter months, while apparent losses range from 8.4–9.3% in summer to 1.3–2.5% in winter. Annual water theft is estimated to be at least 3.6% of system input volume. Spatial variability, which is linked to the elevation and the different urban land uses is proven to play a significant role in the neighborhoods’ water balances and various key performance indicators are suggested and applied for the pressure control scheme. The annual potential savings due to the applied scheme rise up to 51,300 m3 for leakage and 53,730 m3 for pressure-driven demand.
Comparison of Statistical and Machine Learning Models for Pipe Failure Modeling in Water Distribution Networks
Authors: Giraldo-González Mónica Marcela , Rodríguez Juan Pablo
Published: April 2020

The application of statistical and Machine Learning models plays a critical role in planning and decision support processes for efficient and reliable Water Distribution Network (WDN) management. Failure models can provide valuable information for prioritizing system rehabilitation even in data scarcity scenarios, such as developing countries. Few studies have analyzed the performance of more than two models, and examples of case studies in developing countries are insufficient. This study compares various statistical and Machine Learning models to provide useful information to practitioners for the selection of a suitable pipe failure model according to information availability and network characteristics. Three statistical models (i.e., Linear, Poisson, and Evolutionary Polynomial Regressions) were used for failure prediction in groups of pipes. Machine Learning approaches, particularly Gradient-Boosted Tree (GBT), Bayes, Support Vector Machines and Artificial Neuronal Networks (ANNs), were compared in predicting individual pipe failure rates. The proposed approach was applied to a WDN in Bogotá (Colombia). The statistical models showed an acceptable performance (R2 between 0.695 and 0.927), but the Poisson Regression was the most suitable for predicting failures in pipes with lower failure rates. Regarding Machine Learning models, Bayes and ANNs exhibited low performance in the prediction of pipe failure condition. The GBT approach had the best performing classifier.
Biosorption of Water Pollutants by Fungal Pellets
Authors: Legorreta-Castañeda Adriana , Lucho-Constantino Carlos , Beltrán-Hernández Rosa , Coronel-Olivares Claudia , Vázquez-Rodríguez Gabriela
Published: April 2020

Fungal biosorption is an environmental biotechnology based on the ability of the fungal cell wall to concentrate harmful water pollutants. Among its advantages are its simplicity, high efficiency, flexibility of operation, and low cost. The biosorptive performance of fungal pellets is getting growing attention since they offer process advantages over the culture of disperse mycelia, such as an enhanced biomass separation, and a high resilience in severe environmental conditions. In this review, biosorption capacity of fungal pellets towards heavy metals, dyes, phenolic compounds, humic substances, pesticides, and pharmaceuticals was reviewed. Available data about the adsorption capacity of pellets, their removal efficiency, and the operational conditions used were collected and synthesized. The studies relying on biodegradation were discarded to present only the possibilities of fungal pellets for removing these concern pollutants through biosorption. It was found that the biosorption of complex mixtures of pollutants on fungal pellets is scarcely studied, as well as the interfering effect of anions commonly found in water and wastewater. Furthermore, there is a lack of research with real wastewater and at pilot and large scale. These topics need to be further explored to take full advantage of fungal pellets on improving the quality of aquatic systems.
Potential Application of Chilean Natural Zeolite as a Support Medium in Treatment Wetlands for Removing Ammonium and Phosphate from Wastewater
Authors: Vera-Puerto Ismael , Saravia Matias , Olave Jorge , Arias Carlos , Alarcon Erica , Valdes Hugo
Published: April 2020

This study aims to evaluate the sorption characteristics of NH 4 + -N and PO 4 3 − -P onto the surface of natural zeolites coming from Chile and their potential application in the subsurface-flow treatment wetlands for wastewater treatment in rural areas. For this purpose, adsorption experiments onto the zeolite were developed in batch assays. The effects of the adsorbent quantity (20 g and 50 g) and particle size (0.2–1.0 mm; 1.5–3.0 mm, and 5.0–8.0 mm) were evaluated in terms of adsorption capacity at different NH4+-N and PO4−3-P concentrations. Then, the obtained laboratory results were adjusted to theoretical models: Saturation-growth-rate and Langmuir. The saturation adsorption of NH4+-N on the zeolite increases at the same time that the initial concentration increases for the same zeolite quantity; however, the saturation values were similar between the different zeolite sizes tested. For PO4−3-P, the adsorption did not have a direct relationship with the initial concentration nor zeolite quantity and better results were only achieved for zeolite sizes of 1.5–3.0 mm. Regarding the Langmuir model, sizes of 1.5–3.0 mm had the best adsorption characteristics, with the maximum adsorption capacity of up to 1.58 mg/g for NH4+-N and up to 0.08 mg/g for PO4−3-P. Therefore, a new material—a natural zeolite from the Maule Region of Chile—is described as a potential support medium for treatment wetlands.