Miracle-dz/UniFAR-FTUs huggingface dataset:
Serological surveillance of SARS-CoV-2: trends and humoral response in a cohort of public health workers

Background There is considerable debate about the rate of antibody waning after SARS-CoV-2 infection, raising questions around long-term immunity following both natural infection and vaccination. We undertook prospective serosurveillance in a large cohort of healthy adults from the start of the epidemic in England. Methods The serosurveillance cohort included office and laboratory-based staff and healthcare workers in 4 sites in England, who were tested monthly for SARS-CoV-2 spike protein and nucleoprotein IgG between 23rd March and 20th August 2020. Antibody levels from 21 days after a positive test were modelled using mixed effects regression models. Findings In total, 2247 individuals were recruited and 2014 (90%) had 3-5 monthly antibody tests. Overall, 272 (12.1%) of individuals had at least one positive/equivocal spike protein IgG result, with the highest proportion in a hospital site (22%), 14% in London and 2.1% in a rural area. Results were similar for nucleoprotein IgG. Following a positive result, 39/587 (6.6%) tested negative for nucleoprotein IgG and 52/515 (10.1%) for spike protein IgG. Nucleoprotein IgG declined by 6.4% per week (95% CI, 5.5-7.4%; half-life, 75 [95% CI, 66-89] days) and spike protein IgG by 5.8% (95% CI, 5.1-6.6%; half-life, 83 [95% CI, 73-96] days). Conclusions Over the study period SARS-CoV-2 seropositivity was 8-10% overall and up to 21% in clinical healthcare workers. In seropositive individuals, nucleoprotein and spike protein IgG antibodies declined with time after infection and 50% are predicted to fall below the positive test threshold after 6 months.
Turning Up the Dial: the Evolution of a Cybercrime Market Through Set-up, Stable, and Covid-19 Eras

Trust and reputation play a core role in underground cybercrime markets, where participants are anonymous and there is little legal recourse for dispute arbitration. These underground markets exist in tension between two opposing forces: the drive to hide incriminating information, and the trust and stability benefits that greater openness yields. Revealing information about transactions to mitigate scams also provides valuable data about the market. We analyse the first dataset, of which we are aware, about the transactions created and completed on a well-known and high-traffic underground marketplace, Hack Forums, along with the associated threads and posts made by its users over two recent years, from June 2018 to June 2020. We use statistical modelling approaches to analyse the economic and social characteristics of the market over three eras, especially its performance as an infrastructure for trust. In the Set-up era, we observe the growth of users making only one transaction, as well as 'power-users' who make many transactions. In the Stable era, we observe a wide range of activities (including large-scale transfers of intermediate currencies such as Amazon Giftcards) which declines slowly from an initial peak. Finally, we analyse the effects of the Covid-19 pandemic, concluding that while we see a significant increase in transactins across all categories, this reflects a stimulus of the market, rather than a transformation. New users overcome the 'cold start' problem by engaging in low-level currency exchanges to prove their trustworthiness. We observe currency exchange accounts for most contracts, and Bitcoin and PayPal are the preferred payment methods by trading values and number of contracts involved. The market is becoming more centralised over time around influential users and threads, with significant changes observed during the Set-up and Covid-19 eras.
An evaluation of natural and synthetic vitamin E supplementation on growth performance and antioxidant capacity of broilers in early age

Abstract: The effects of natural (d-α-tocopherol) and synthetic (dl-α-tocopherol acetate) vitamin E on growth performance and antioxidant capacity of broilers in early age were investigated. A total of 144 one-day-old Arbor Acres broilers were randomly divided into three treatments (48 birds in each treatment). The birds in the control group were fed the basal diet whereas those in the treatment groups were fed basal diets supplemented with 20 IU kg-1 dl-α-tocopherol acetate or 20 IU kg-1 d-α-tocopherol for 21 d, respectively. Vitamin E supplementation, irrespective of source, significantly increased (P < 0.05) the α-tocopherol concentrations in jejunum and ileum, as well as activities of plasma total superoxide dismutase, hepatic glutathione peroxidase (GSH-PX), and ileal GSH-PX; however, the extent to increase hepatic α-tocopherol concentration was more pronounced when the source of vitamin E was natural form (P < 0.05). In addition, dietary natural vitamin E supplementation significantly increased (P < 0.05) the concentration of plasma α-tocopherol as compared with the control group, whereas the similar effect was not observed in birds given the diet supplemented with synthetic vitamin E (P > 0.05). In conclusion, dietary vitamin E supplementation, especially natural form, could enhance the antioxidant capacity and α-tocopherol accumulation of broilers in early age.
Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization

Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.
Effects of Exogenous Organic Acids on Cd Tolerance Mechanism of Salix variegata Franch. Under Cd Stress

Chelate induction of organic acids has been recognized to enhance metal uptake and translocation in plants, but the underlying mechanism remains unclear. In this study, seedlings of Salix variegata were hydroponically exposed to the combinations of Cd (0 and 50 μM) and three exogenous organic acids (100 μM of citric, tartaric, or malic acid). Plant biomass, antioxidant enzymes, non-protein thiol compounds (NPT) content, and the expression of candidate genes associated with Cd accumulation and tolerance were determined. Results showed that Cd significantly inhibited plant biomass but stimulated the activity of antioxidant enzymes in the roots and leaves, while the lipid peroxidation increased as well. Respective addition of three organic acids greatly enhanced plant resistance to oxidative stress and reduced the lipid peroxidation induced by Cd, with the effect of malic acid showing greatest. The addition of organic acids also significantly increased the content of glutathione in the root, further improving the antioxidant capacity and potential of phytochelatin biosynthesis. Moreover, Cd induced the expression level of candidate genes in roots of S. variegata. The addition of three organic acids not only promoted the expression of candidate genes but also drastically increased Cd accumulation in S. variegata. In summary, application of citric, tartaric, or malic acid alleviated Cd-imposed toxicity through the boost of enzymatic and non-enzymatic antioxidants and candidate gene expression, while their effects on Cd tolerance and accumulation of S. variegata differed.
Interactions Between Therapeutics for Metabolic Disease, Cardiovascular Risk Factors, and Gut Microbiota

With improved standards of living, the incidence of multiple metabolic disorders has increased year by year, especially major risk factors for cardiovascular disease such as hyperglycemia and hyperlipidemia, continues to increase. Emerging epidemiological data and clinical trials have shown the additional protective effects of some metabolic therapy drugs against cardiovascular diseases. A series of studies have found that these drugs may work by modulating the composition of gut microbiota. In this review, we provide a brief overview of the contribution of the gut microbiota to both metabolic disorders and cardiovascular diseases, as well as the response of gut microbiota to metabolic therapy drugs with cardiovascular benefits. In this manner, we link the recent advances in microbiome studies on metabolic treatment drugs with their cardiovascular protective effects, suggesting that intestinal microorganisms may play a potential role in reducing cardiovascular risk factors. We also discuss the potential of microorganism-targeted therapeutics as treatment strategies for preventing and/or treating cardiovascular disease and highlight the need to establish causal links between therapeutics for metabolic diseases, gut microbiota modulation, and cardiovascular protection.
When Push Comes to Ads: Measuring the Rise of (Malicious) Push Advertising

The rapid growth of online advertising has fueled the growth of ad-blocking software, such as new ad-blocking and privacy-oriented browsers or browser extensions. In response, both ad publishers and ad networks are constantly trying to pursue new strategies to keep up their revenues. To this end, ad networks have started to leverage the Web Push technology enabled by modern web browsers. As web push notifications (WPNs) are relatively new, their role in ad delivery has not yet been studied in depth. Furthermore, it is unclear to what extent WPN ads are being abused for malvertising (i.e., to deliver malicious ads). In this paper, we aim to fill this gap. Specifically, we propose a system called PushAdMiner that is dedicated to (1) automatically registering for and collecting a large number of web-based push notifications from publisher websites, (2) finding WPN-based ads among these notifications, and (3) discovering malicious WPN-based ad campaigns. Using PushAdMiner, we collected and analyzed 21,541 WPN messages by visiting thousands of different websites. Among these, our system identified 572 WPN ad campaigns, for a total of 5,143 WPN-based ads that were pushed by a variety of ad networks. Furthermore, we found that 51% of all WPN ads we collected are malicious, and that traditional ad-blockers and URL filters were mostly unable to block them, thus leaving a significant abuse vector unchecked.
Understanding the Role of the Hypervariable Region in the Open Reading Frame 1 of the Hepatitis E virus in Viral Replication

Hepatitis E virus (HEV) is a major cause of enterically transmitted acute viral hepatitis in developing countries that lack proper hygienic infrastructure. Hepatitis E is globally distributed and has emerged as an important public health disease in both developing and industrialized countries. HEV is a non-enveloped virus carrying a single-stranded positive-sense RNA genome of approximately 7.200 bp in length. The life cycle of HEV is poorly understood due to the lack of an efficient cell culture system. Animal model systems, including non-human primates, swine, and chickens are being used to study some fundamental aspects of the HEV biology. Recently, novel animal strains of rat and rabbit HEV have been discovered, and whose usage as animal model systems needs to be established. HEV infections in pigs and chickens provide excellent model systems to study the replication and pathogenesis aspects of HEV. Recently, we identified a hypervariable region (HVR) in the open reading frame 1 (ORF1) of HEV. The objectives of this dissertation were to utilize chicken and swine model systems to study the role of HVR in HEV infection in vivo, to determine the effects of HVR on replication of HEV in vitro, and to analyze the effect of exchange of HVR among different genotypes on the replication-competency and virion production in vitro. Extensive sequence variability in the HVR among HEV strains of different genotypes prompted us to study the dispensability of this region. Initially we constructed two partial deletion mutants of genotype 1 human HEV, hHVRd1 and hHVRd2, with in-frame deletion of amino acids (aa) 711 to 777 and 747 to 761 in the HVR of a sub-genomic GFP HEV replicon. Expression of enhanced green fluorescent protein by the mutant hHVRd2 confirmed the dispensability of amino acid residues 747-761 of the HVR. To confirm our in vitro results, specific-pathogen-free (SPF) chickens were intra-hepatically inoculated with capped RNA transcripts from three avian HEV HVR-deletion mutants: mutants aHVRd1 (Δ557-585), aHVRd2 (Δ612-641), and aHVRd3 (Δ557-641). Chickens intra-hepatically inoculated with the
A Bacterial Epigenetic Switch in Non-typeable Haemophilus influenzae Modifies Host Immune Response During Otitis Media

Non-typeable Haemophilus influenzae (NTHi) causes multiple diseases of the human airway and is a predominant bacterial pathogen of acute otitis media and otitis media in which treatment fails. NTHi utilizes a system of phase variable epigenetic regulation, termed the phasevarion, to facilitate adaptation and survival within multiple sites of the human host. The NTHi phasevarion influences numerous disease-relevant phenotypes such as biofilm formation, antibiotic resistance, and opsonization. We have previously identified an advantageous selection for a specific phasevarion status, which significantly affects severity and chronicity of experimental otitis media. In this study, we utilized pure cultures of NTHi variants in which modA was either locked ON or locked OFF, and thus modA was unable to phase vary. These locked variants were used to assess the progression of experimental otitis media and define the specific immune response induced by each subpopulation. Although the initial disease caused by each subpopulation was similar, the immune response elicited by each subpopulation was unique. The modA2 OFF variant induced significantly greater activation of macrophages both in vitro and within the middle ear during disease. In contrast, the modA2 ON variant induced a greater neutrophil extracellular trap response, which led to greater killing of the modA2 ON variant. These data suggest that not only does the NTHi phasevarion facilitate adaptation, but also allows the bacteria to alter immune responses during disease. Understanding these complex bacterial-host interactions and the regulation of bacterial factors responsible is critical to the development of better diagnostic, treatment, and preventative strategies for these bacterial pathogens.
Retinal characterization in the eyes of two bats endemic in the Egyptian fauna, the Egyptian fruit bat (Rousettus aegyptiacus) and insectivorous bat (Pipistrellus kuhlii), using the light microscope and transmission electron microscope

Bats are the only mammals that can fly in the dark without eye usage. This study was conducted to describe the structural and functional adaptations of the retina of two bats very common in the Egyptian fauna having a different lifestyle: the Egyptian fruit bat (Rousettus aegyptiacus) and insectivorous bat (Pipistrellus kuhlii). Seven eyes were collected from adult individuals of each species. Examination of the retina using a light microscope and a transmission electron microscope was carried out. The retina of P. kuhlii was thicker than that of R. aegyptiacus, which had many projections extended from the choroid layer into retina forming papillae. Despite rods being dominant in retinae of both species, cone photoreceptors were encountered in both retinae. The outer plexiform layer of R. aegyptiacus was arranged into islets between the outer nuclear layer produced differences in its thickness. However, the retina of P. kuhlii showed a normal arrangement of retinal structure. The retinal pigment epithelium of both bat species consists of a single layer of the cuboidal cells with a round to oval vesicular nuclei, which showed a lack of pigmentation in R. aegyptiacus and poor pigmentation in the P. kuhlii. In conclusion, our investigation detected many structural and ultrastructural differences between the two bat species. The presence of many projections protruded from the choroid layer of R. aegyptiacus retina is considered the most characteristic difference between the retinae of R. aegyptiacus and P. kuhlii.
The Cell Wall of Seagrasses: Fascinating, Peculiar and a Blank Canvas for Future Research

Seegrasses are a polyphyletic group of angiosperm plants, which evolved from early monocotyledonous land plants and returned to the marine environment around 140 million years ago. Today, seagrasses comprise the five families Zosteraceae, Hydrocharitaceae, Posidoniaceae, Cymodoceaceae, and Ruppiaceae and form important coastal ecosystems worldwide. Despite of this ecological importance, the existing literature on adaption of these angiosperms to the marine environment and especially their cell wall composition is limited up to now. A unique feature described for some seagrasses is the occurrence of polyanionic, low-methylated pectins mainly composed of galacturonic acid and apiose (apiogalacturonans). Furthermore, sulfated galactans have been detected in some species. Recently, arabinogalactan-proteins (AGPs), highly glycosylated proteins of the cell wall of land plants, have been isolated for the first time from a seagrass of the baltic sea. Obviously, seagrass cell walls are characterized by new combinations of structural polysaccharide and glycoprotein elements known from macroalgae and angiosperm land plants. In this review, current knowledge on cell walls of seagrasses is summarized and suggestions for future investigations are given.
Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic

In this study, we analyzed full-length SARS-CoV-2 genomes from multiple countries to determine early trends in the evolutionary dynamics of the novel COVID-19 pandemic. Results indicated SARS-CoV-2 evolved early into at least three phylogenetic groups, characterized by positive selection at specific residues of the accessory proteins ORF3a and ORF8. Also, we are reporting potential relevant sites under positive selection at specific sites of non-structural proteins nsp6 and helicase. Our analysis of co-evolution showed evidence of epistatic interactions among sites in the genome that may be important in the generation of variants adapted to humans. These observations might impact not only public health but also suggest that more studies are needed to understand the genetic mechanisms that may affect the development of therapeutic and preventive tools, like antivirals and vaccines. Collectively, our results highlight the identification of ongoing selection even in a scenario of conserved sequences collected over the first 3 months of this pandemic.
A Comprehensive Update on the Chylomicronemia Syndrome

The chylomicronemia syndrome is characterized by severe hypertriglyceridemia and fasting chylomicronemia and predisposes affected individuals to acute pancreatitis. When due to very rare monogenic mutations in the genes encoding the enzyme, lipoprotein lipase, or its regulators, APOC2, APOA5, GPIHBP1, and LMF1, it is referred to as the familial chylomicronemia syndrome. Much more frequently, the chylomicronemia syndrome results from a cluster of minor genetic variants causing polygenic hypertriglyceridemia, which is exacerbated by conditions or medications which increase triglyceride levels beyond the saturation point of triglyceride removal systems. This situation is termed the multifactorial chylomicronemia syndrome. These aggravating factors include common conditions such as uncontrolled diabetes, overweight and obesity, alcohol excess, chronic kidney disease and pregnancy and several medications, including diuretics, non-selective beta blockers, estrogenic compounds, corticosteroids, protease inhibitors, immunosuppressives, antipsychotics, antidepressants, retinoids, L-asparaginase, and propofol. A third uncommon cause of the chylomicronemia syndrome is familial forms of partial lipodystrophy. Development of pancreatitis is the most feared complication of the chylomicronemia syndrome, but the risk of cardiovascular disease as well as non-alcoholic steatohepatitis is also increased. Treatment consists of dietary fat restriction and weight reduction combined with the use of triglyceride lowering medications such as fibrates, omega 3 fatty acids and niacin. Effective management of aggravating factors such as improving diabetes control, discontinuing alcohol and replacing or reducing the dose of medications that raise triglyceride levels is essential. Importantly, many if not most cases of the chylomicronemia syndrome can be prevented by effective identification of polygenic hypertriglyceridemia in people with conditions that increase its likelihood or before starting medications that may increase triglyceride levels. Several new pharmacotherapeutic agents are being tested that are likely to considerably improve treatment of hypertriglyceridemia in people at risk.