Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Prophylactic HPV Vaccines on Oral and Oropharyngeal HPV Infection—A Systematic Review

Human papillomavirus (HPV) imposes an increased risk of developing cervical, anal and oropharyngeal cancer. In the Western world, HPV infection is currently the major cause of oropharyngeal cancer. The effectiveness of HPV vaccines for oral or oropharyngeal HPV infection is yet to be determined. This study conducted a systematic literature search in Pubmed and Embase. Studies investigating the impact of HPV vaccines on oral or oropharyngeal HPV infection were enrolled. This review reports the relative prevention percentage (RPP), including a risk of bias assessment as well as a quality assessment study. Nine studies were included (48,777 participants): five cross-sectional studies; one randomized community trial study (RCT); one longitudinal cohort study; and two case-control studies. A significant mean RPP of 83.9% (66.6–97.8%) was calculated from the cross-sectional studies, 82.4% in the included RCT and 83% in the longitudinal cohort study. Further, two case-control studies that measured antibody response in participants immunized with HPV vaccines were included. Respectively, 100% and 93.2% of participants developed HPV-16 Immunoglobulin G (IgG) antibodies in oral fluids post-vaccination. Analysis of the studies identified a significant decrease in vaccine-type oral or oropharyngeal HPV infections in study participants immunized with HPV vaccines across study designs and heterogenous populations. Further, a significant percentage of participants developed IgG antibodies in oral fluid post-vaccination.
Extra-Corporeal Membrane Oxygenation Cadaver Donors: What about Tissues Used as Allografts?

Several studies demonstrated the efficacy of post-mortem extracorporeal membrane oxygenation (ECMO) on donors in preserving organ function addressing organ transplantation. Nevertheless, no common and shared evidence was reached about the possibility of using ECMO donors in tissue harvesting. Therefore, this work aimed first to review the current scientific literature about ECMO donors, and then to focus on the use of ECMO tissues as allografts, mainly addressing musculoskeletal tissues, which are of the most interest for reconstruction. A search was conducted on the current scientific literature, focusing on the keywords “ECMO” and “Donor”. Several online databases were used, including PubMed, Scopus, and Web of Science. From the preliminary search, 478 articles were obtained, out of which 173 specifically reported the use of ECMO for donation and transplantation purposes. Literature reported extensive analyses of ECMO organs—overall from the abdomen—both in pre- and post-transplantation studies. On the other hand, ECMO tissues were explanted only in a very limited number of cases; moreover, no information was referred about their status and use. A revision of the current scientific literature highlighted the lack of information concerning ECMO tissues and the necessity to perform preclinical, ex vivo studies to compare allografts from ECMO donors, with respect to standard donors, and, thus, to verify whether they can be harvested and implanted safely and with efficacy.
A Microencapsulated Mixture of Eugenol and Garlic Tincture Supplementation Mitigates the Effect of Necrotic Enteritis on Intestinal Integrity and Increases Goblet Cells in Broilers

This study was conducted to examine the effects of a plant extract mixture, a microencapsulated product composed of eugenol and garlic tincture (PE), on intestinal health in broilers under necrotic enteritis (NE) challenge. A total of 960 d-old mixed-sex Cobb 500 chicks were randomly distributed to 48-floor pens housing 20 birds per pen. Six treatments were applied: UC, unchallenged control; CC, challenged control; PE, challenged group plus PE; AM, challenged group plus antimicrobial (AM); FAP, challenged group plus a full dose of AM with PE; HAP, challenged group plus a half dose of AM with PE in starter, grower and finisher phases. Birds in the challenged groups were inoculated with Eimeria spp. on d 9 and Clostridium perfringens on d 14. On d 16, the CC group had increased serum fluorescein isothiocyanate dextran (FITC-d), reduced villus surface area, goblet cell number, upregulated CLDN1, JAM2 genes and reduced microbial diversity compared to the UC group (p < 0.05). Birds fed PE had reduced FITC-d, increased goblet cell number and Bifidobacterium compared to the CC group (p < 0.05). Birds fed PE had reduced CLDN5 expression in male birds, and Bacteroides spp. in female birds than CC group (p < 0.05). These findings suggest that PE supplementation mitigates the effect of NE by improving the intestinal health of birds.
No Evidence for Seed Transmission of Tomato Yellow Leaf Curl Sardinia Virus in Tomato

Seed transmission is an important factor in the epidemiology of plant pathogens. Geminiviruses are serious pests spread in tropical and subtropical regions. They are transmitted by hemipteran insects, but a few cases of transmission through seeds were recently reported. Here, we investigated the tomato seed transmissibility of the begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), one of the agents inducing the tomato yellow leaf curl disease, heavily affecting tomato crops in the Mediterranean area. None of the 180 seedlings originating from TYLCSV-infected plants showed any phenotypic alteration typical of virus infection. Moreover, whole viral genomic molecules could not be detected in their cotyledons and true leaves, neither by membrane hybridization nor by rolling-circle amplification followed by PCR, indicating that TYLCSV is not a seed-transmissible pathogen for tomato. Examining the localization of TYLCSV DNA in progenitor plants, we detected the virus genome by PCR in all vegetative and reproductive tissues, but viral genomic and replicative forms were found only in leaves, flowers and fruit flesh, not in seeds and embryos. Closer investigations allowed us to discover for the first time that these embryos were superficially contaminated by TYLCSV DNA but whole genomic molecules were not detectable. Therefore, the inability of TYLCSV genomic molecules to colonize tomato embryos during infection justifies the lack of seed transmissibility observed in this host.
Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host–Pathogen Interactions

Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy.
Longitudinal Characterization of the Gut Bacterial and Fungal Communities in Yaks

Development phases are important in maturing immune systems, intestinal functions, and metabolism for the construction, structure, and diversity of microbiome in the intestine during the entire life. Characterizing the gut microbiota colonization and succession based on age-dependent effects might be crucial if a microbiota-based therapeutic or disease prevention strategy is adopted. The purpose of this study was to reveal the dynamic distribution of intestinal bacterial and fungal communities across all development stages in yaks. Dynamic changes (a substantial difference) in the structure and composition ratio of the microbial community were observed in yaks that matched the natural aging process from juvenile to natural aging. This study included a significant shift in the abundance and proportion of bacterial phyla (Planctomycetes, Firmicutes, Bacteroidetes, Spirochaetes, Tenericutes, Proteobacteria, and Cyanobacteria) and fungal phyla (Chytridiomycota, Mortierellomycota, Neocallimastigomycota, Ascomycota, and Basidiomycota) across all development stages in yaks. As yaks grew older, variation reduced, and diversity increased as compared to young yaks. In addition, the intestine was colonized by a succession of microbiomes that coalesced into a more mature adult, including Ruminococcaceae_UCG-005, Romboutsia, Prevotellaceae_UCG-004, Blautia, Clostridium_sensu_stricto_1, Ruminococcus_1, Ruminiclostridium_5, Rikenellaceae_RC9_gut_group, Alloprevotella, Acetitomaculum, Lachnospiraceae_NK3A20_group, Bacteroides, Treponema_2, Olsenella, Escherichia-Shigella, Candidatus_Saccharimonas, and fungal communities Mortierella, Lomentospora, Orpinomyces, and Saccharomyces. In addition, microorganisms that threaten health, such as Escherichia-Shigella, Mortierella, Lomentospora and Hydrogenoanaerobacterium, Corynebacterium_1, Trichosporon, and Coprinellus, were enriched in young and old yaks, respectively, although all yaks were healthy. The significant shifts in microflora composition and structure might reflect adaptation of gut microbiome, which is associated with physicochemical conditions changes and substrate availability in the gut across all development periods of yaks.
AtfA-Independent Adaptation to the Toxic Heavy Metal Cadmium in Aspergillus nidulans

Cadmium is an exceptionally toxic industrial and environmental pollutant classified as a human carcinogen. In order to provide insight into how we can keep our environment safe from cadmium contamination and prevent the accumulation of it in the food chain, we aim to elucidate how Aspergillus nidulans, one of the most abundant fungi in soil, survives and handles cadmium stress. As AtfA is the main transcription factor governing stress responses in A. nidulans, we examined genome-wide expression responses of wild-type and the atfA null mutant exposed to CdCl2. Both strains showed up-regulation of the crpA Cu2+/Cd2+ pump gene and AN7729 predicted to encode a putative bis(glutathionato)-cadmium transporter, and transcriptional changes associated with elevated intracellular Cys availability leading to the efficient adaptation to Cd2+. Although the deletion of atfA did not alter the cadmium tolerance of the fungus, the cadmium stress response of the mutant differed from that of a reference strain. Promoter and transcriptional analyses of the “Phospho-relay response regulator” genes suggest that the AtfA-dependent regulation of these genes can be relevant in this phenomenon. We concluded that the regulatory network of A. nidulans has a high flexibility allowing the fungus to adapt efficiently to stress both in the presence and absence of this important transcription factor.
Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.
Synthetic Data in Quantitative Scanning Probe Microscopy

Synthetic data are of increasing importance in nanometrology. They can be used for development of data processing methods, analysis of uncertainties and estimation of various measurement artefacts. In this paper we review methods used for their generation and the applications of synthetic data in scanning probe microscopy, focusing on their principles, performance, and applicability. We illustrate the benefits of using synthetic data on different tasks related to development of better scanning approaches and related to estimation of reliability of data processing methods. We demonstrate how the synthetic data can be used to analyse systematic errors that are common to scanning probe microscopy methods, either related to the measurement principle or to the typical data processing paths.
Evaluation of the Erosive and Cariogenic Potential of Over-the-Counter Pediatric Liquid Analgesics and Antipyretics

To evaluate the cariogenic and erosive potentials of over-the-counter pediatric oral liquid antipyretics and analgesics, we tested nine over-the-counter pediatric oral liquid medications classified as antipyretic or analgesic medicines available in Korea. For each substance, we measured the pH with a pH meter and the sugar content with a sugar content meter. We determined the titratable acidity (TA) levels based on the volumes of NaOH solution that had to be added to reach a pH of 7.0. We also evaluated the dental erosion potentials with an International Organization for Standardization method based on observing changes in the pH of a CaPO4 solution upon introducing a small volume of the solution to be tested. The oral liquid medications had pH values of 3.40–5.68. In the TA assessments, several oral liquid medications required greater volumes of NaOH solution to reach a pH of 7.0. The dental erosion potentials varied but correlated strongly with the NaOH volumes needed to reach a neutral pH (r = 0.84; p < 0.0001). Many oral liquid antipyretics and analgesics have features that can promote dental erosion. A correct understanding of pediatric antipyretics and analgesics is required in dentistry for children’s oral health.
Effect of Different Species of Prorocentrum Genus on the Japanese Oyster Crassostrea gigas Proteomic Profile

This paper assesses the effects of exposure to toxic concentrations (1200 to 6000 cells/mL) of the dinoflagellates Prorocentrum lima, Prorocentrum minimum, and Prorocentrum rhathymum and several concentrations of aqueous and organic extracts obtained from the same species (0 to 20 parts per thousand) on the Crassostrea gigas (5–7 mm) proteomic profile. Through comparative proteomic map analyses, several protein spots were detected with different expression levels, of which eight were selected to be identified by liquid chromatography–mass spectrometry (LC–MS/MS) analyses. The proteomic response suggests that, after 72 h of exposure to whole cells, the biological functions of C. gigas affected proteins in the immune system, stress response, contractile systems and cytoskeletal activities. The exposure to organic and aqueous extracts mainly showed effects on protein expressions in muscle contraction and cytoskeleton morphology. These results enrich the knowledge on early bivalve developmental stages. Therefore, they may be considered a solid base for new bioassays and/or generation of specific analytical tools that allow for some of the main effects of algal proliferation phenomena on bivalve mollusk development to be monitored, characterized and elucidated.
Addition of Honey to an Apple and Passion Fruit Mixed Beverage Improves Its Phenolic Compound Profile

The addition of honey to mixed beverages is interesting due to its contribution to the sweet taste, as well as because it is a dietary source of bioactive compounds. In this study, we investigated the chemical composition and sensory acceptance of an apple and passion fruit mixed beverage with added honey. The addition of honey did not produce a noticeable change in instrumental color but led to an increase in total soluble solids contents, and FRAP (20%), TEAC (72%), and DPPH (62%) values. The honey mixed beverages exhibited a better phenolic compound profile with an increase in catechin contents and an enrichment of quercetin when compared to the control mixed beverage, as well presenting good sensory acceptance. In conclusion, our results show that the addition of honey can be an alternative for improving the nutritional and sensorial characteristics of an apple and passion fruit mixed beverage.
Skin Color Retention in Red Potatoes during Long-Term Storage with Edible Coatings

In this study, we aimed to investigate the effect of edible coatings and cold storage conditions on the skin color of red potatoes (Ciklamen and Modoc) stored for six months at 4 ± 2 °C and 90 ± 5% relative humidity (RH). The four different formulations used were sodium alginate (F1), sodium alginate and potato starch (F2), zein and chitosan (F3), and chitosan, sodium alginate and potato starch (F4), in addition to the control treatment with distilled water. The treated samples were assessed periodically during six months of storage for changes in color, levels of reducing sugars, total phenolics and sensory qualities. The results indicated that the treatment with edible coatings significantly enhanced the chroma value of skin color, especially F1 and F2 formulations. However, these coatings instilled a limited effect on the level of reducing sugars. Moreover, F1 and F4 formulations exerted a significant effect (p < 0.05) on anthocyanin content examined after three months of storage. Alginate-based edible coatings significantly improved sensory evaluation, especially in terms of the color, gloss, and general acceptability of red skin potatoes.
Preparation and Sustained-Release Performance of PLGA Microcapsule Carrier System

Microcapsules have been widely studied owing to their biocompatibility and potential for application in various areas, particularly drug delivery. However, the size of microcapsules is difficult to control, and the size distribution is very broad via various encapsulation techniques. Therefore, it is necessary to obtain microcapsules with uniform and tailored size for the construction of controlled-release drug carriers. In this study, emulsification and solvent evaporation methods were used to prepare a variety of ovalbumin-loaded poly (lactic-co-glycolic acid) (PLGA) microcapsules to determine the optimal preparation conditions. The particle size of the PLGA microcapsules prepared using the optimum conditions was approximately 200 nm, which showed good dispersibility with an ovalbumin encapsulation rate of more than 60%. In addition, porous microcapsules with different pore sizes were prepared by adding a varying amount of porogen bovine serum albumin (BSA) to the internal water phase. The release curve showed that the rate of protein release from the microcapsules could be controlled by adjusting the pore size. These findings demonstrated that we could tailor the morphology and structure of microcapsules by regulating the preparation conditions, thus controlling the encapsulation efficiency and the release performance of the microcapsule carrier system. We envision that this controlled-release novel microcapsule carrier system shows great potential for biomedical applications.
Rifampicin–Liposomes for Mycobacterium abscessus Infection Treatment: Intracellular Uptake and Antibacterial Activity Evaluation

Treatment of pulmonary infections caused by Mycobacterium abscessus are extremely difficult to treat, as this species is naturally resistant to many common antibiotics. Liposomes are vesicular nanocarriers suitable for hydrophilic and lipophilic drug loading, able to deliver drugs to the target site, and successfully used in different pharmaceutical applications. Moreover, liposomes are biocompatible, biodegradable and nontoxic vesicles and nebulized liposomes are efficient in targeting antibacterial agents to macrophages. The present aim was to formulate rifampicin-loaded liposomes (RIF–Lipo) for lung delivery, in order to increase the local concentration of the antibiotic. Unilamellar liposomal vesicles composed of anionic DPPG mixed with HSPC for rifampicin delivery were designed, prepared, and characterized. Samples were prepared by using the thin-film hydration method. RIF–Lipo and unloaded liposomes were characterized in terms of size, ζ-potential, bilayer features, stability and in different biological media. Rifampicin’s entrapment efficiency and release were also evaluated. Finally, biological activity of RIF-loaded liposomes in Mycobacterium abscessus-infected macrophages was investigated. The results show that RIF-lipo induce a significantly better reduction of intracellular Mycobacterium abscessus viability than the treatment with free drug. Liposome formulation of rifampicin may represent a valuable strategy to enhance the biological activity of the drug against intracellular mycobacteria.
Two-Pore Channels Regulate Expression of Various Receptors and Their Pathway-Related Proteins in Multiple Ways

Two-pore channels (TPCs) constitute a small family of ion channels within membranes of intracellular acidic compartments, such as endosomes and lysosomes. They were shown to provide transient and locally restricted Ca2+-currents, likely responsible for fusion and/or fission events of endolysosomal membranes and thereby for intracellular vesicle trafficking. Genetic deletion of TPCs not only affects endocytosis, recycling, and degradation of various surface receptors but also uptake and impact of bacterial protein toxins and entry and intracellular processing of some types of viruses. This review points to important examples of these trafficking defects on one part but mainly focuses on the resulting impact of the TPC inactivation on receptor expression and receptor signaling. Thus, a detailed RNA sequencing analysis using TPC1-deficient fibroblasts uncovered a multitude of changes in the expression levels of surface receptors and their pathway-related signaling proteins. We refer to several classes of receptors such as EGF, TGF, and insulin as well as proteins involved in endocytosis.