Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell-Type Apoptosis in Lung during SARS-CoV-2 Infection

The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown. In the present study, we examined apoptosis in postmortem lung sections from COVID-19 patients and in lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence assays and Western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with a novel non-cyclic nucleotide small molecule EPAC1-specific activator reduced apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.
Evaluation of Aerosol Therapy during the Escalation of Care in a Model of Adult Cystic Fibrosis

Lung disease is the main cause of morbidity and mortality in cystic fibrosis (CF). CF patients inhale antibiotics regularly as treatment against persistent bacterial infections. The goal of this study was to investigate the effect of clinical intervention on aerosol therapy during the escalation of care using a bench model of adult CF. Droplet size analysis of selected antibiotics was completed in tandem with the delivered aerosol dose (% of total dose) assessments in simulations of various interventions providing oxygen supplementation or ventilatory support. Results highlight the variability of aerosolised dose delivery. In the homecare setting, the vibrating mesh nebuliser (VMN) delivered significantly more than the jet nebuliser (JN) (16.15 ± 0.86% versus 6.51 ± 2.15%). In the hospital setting, using VMN only, significant variability was seen across clinical interventions. In the emergency department, VMN plus mouthpiece (no supplemental oxygen) was seen to deliver (29.02 ± 1.41%) versus low flow nasal therapy (10 L per minute (LPM) oxygen) (1.81 ± 0.47%) and high flow nasal therapy (50 LPM oxygen) (3.36 ± 0.34%). In the ward/intensive care unit, non-invasive ventilation recorded 19.02 ± 0.28%, versus 22.64 ± 1.88% of the dose delivered during invasive mechanical ventilation. These results will have application in the design of intervention-appropriate aerosol therapy strategies and will be of use to researchers developing new therapeutics for application in cystic fibrosis and beyond.
Fiber-Templated 3D Calcium-Phosphate Scaffolds for Biomedical Applications: The Role of the Thermal Treatment Ambient on Physico-Chemical Properties

A successful bone-graft-controlled healing entails the development of novel products with tunable compositional and architectural features and mechanical performances and is, thereby, able to accommodate fast bone in-growth and remodeling. To this effect, graphene nanoplatelets and Luffa-fibers were chosen as mechanical reinforcement phase and sacrificial template, respectively, and incorporated into a hydroxyapatite and brushite matrix derived by marble conversion with the help of a reproducible technology. The bio-products, framed by a one-stage-addition polymer-free fabrication route, were thoroughly physico-chemically investigated (by XRD, FTIR spectroscopy, SEM, and nano-computed tomography analysis, as well as surface energy measurements and mechanical performance assessments) after sintering in air or nitrogen ambient. The experiments exposed that the coupling of a nitrogen ambient with the graphene admixing triggers, in both compact and porous samples, important structural (i.e., decomposition of β-Ca3(PO4)2 into α-Ca3(PO4)2 and α-Ca2P2O7) and morphological modifications. Certain restrictions and benefits were outlined with respect to the spatial porosity and global mechanical features of the derived bone scaffolds. Specifically, in nitrogen ambient, the graphene amount should be set to a maximum 0.25 wt. % in the case of compact products, while for the porous ones, significantly augmented compressive strengths were revealed at all graphene amounts. The sintering ambient or the graphene addition did not interfere with the Luffa ability to generate 3D-channels-arrays at high temperatures. It can be concluded that both Luffa and graphene agents act as adjuvants under nitrogen ambient, and that their incorporation-ratio can be modulated to favorably fit certain foreseeable biomedical applications.
Sequence, Chromatin and Evolution of Satellite DNA

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
Role of Virally-Encoded Deubiquitinating Enzymes in Regulation of the Virus Life Cycle

The ubiquitin (Ub) proteasome system (UPS) plays a pivotal role in regulation of numerous cellular processes, including innate and adaptive immune responses that are essential for restriction of the virus life cycle in the infected cells. Deubiquitination by the deubiquitinating enzyme, deubiquitinase (DUB), is a reversible molecular process to remove Ub or Ub chains from the target proteins. Deubiquitination is an integral strategy within the UPS in regulating survival and proliferation of the infecting virus and the virus-invaded cells. Many viruses in the infected cells are reported to encode viral DUB, and these vial DUBs actively disrupt cellular Ub-dependent processes to suppress host antiviral immune response, enhancing virus replication and thus proliferation. This review surveys the types of DUBs encoded by different viruses and their molecular processes for how the infecting viruses take advantage of the DUB system to evade the host immune response and expedite their replication.
The Repurposing of Acetylsalicylic Acid as a Photosensitiser to Inactivate the Growth of Cryptococcal Cells

Photodynamic treatment (PDT) is often successful when used against aerobic microbes, given their natural susceptibility to oxidative damage. To this end, the current study aimed to explore the photodynamic action of acetylsalicylic acid (ASA; aspirin, which is commonly used to treat non-infectious ailments), when administered to respiring cryptococcal cells. The treatment of cryptococcal cells, i.e., exposure to 0.5 or 1 mM of ASA in the presence of ultraviolet light (UVL) for 10 min, resulted in a significant (p < 0.05) reduction in the growth of tested cells when compared to non-treated (non-Rx) cells, i.e., no ASA and no UVL. The treated cells were also characterised by diseased mitochondria, which is crucial for the survival of respiring cells, as observed by a significant (p < 0.05) loss of mitochondrial membrane potential (ΔΨM) and significant (p < 0.05) accumulation of reactive oxygen species (ROS) when compared to non-Rx cells. Moreover, the photolytic products of acetylsalicylic acid altered the ultrastructural appearance of treated cells as well as limited the expression levels of the capsular-associated gene, CAP64, when compared to non-Rx cells. The results of the study highlight the potential use of ASA as a photosensitiser that is effective for controlling the growth of cryptococcal cells. Potentially, this treatment can also be used as an adjuvant, to complement and support the usage of current anti-microbial agents.
Molecular and Serological Detection of Piroplasms in Horses from Nigeria

Equine piroplasmosis, an economically important disease of equids caused by the hemoprotozoan parasites Theileria equi, T. haneyi, and Babesia caballi, has a worldwide distribution. These parasites are transmitted by ixodid ticks. To improve the detection of horses in Nigeria exposed to piroplasm parasites, 72 horses with variable clinical signs of piroplasmosis were sampled from Northwest and Northcentral Nigeria and tested by nPCR and cELISA. Blood and serum samples were collected from each horse via jugular venesection. Individually, nPCR or cELISA failed to identify all horses exposed to piroplasms. A combination of species-specific nPCR and the OIE-approved T. equi and B. caballi cELISAs enhanced the detection of horses exposed to parasites. The results also demonstrated horses showing abnormal hematology were positive for only T. equi, except for one sample that was coinfected with T. equi and T. haneyi. We also identified ticks collected from some of the horses, with Rhipicephalus evertsi evertsi being the most prevalent. This study shows that a larger proportion of horses in the sample set were exposed to T. equi than B. caballi or T. haneyi. Additionally, ticks that have been previously reported as potential vectors for these parasites were found to have infested sampled horses. Further studies are needed to investigate which tick species are competent vectors for Theileria spp. and Babesia caballi in Nigeria.
Surveillance for Enteroviruses Associated with Hand, Foot, and Mouth Disease, and Other Mucocutaneous Symptoms in Spain, 2006–2020

Hand, foot, and mouth disease (HFMD) is a mild illness caused by enteroviruses (EV), although in some Asian countries, large outbreaks have been reported in the last 25 years, with a considerable incidence of neurological complications. This study describes epidemiological and clinical characteristics of EV infections involved in HFMD and other mucocutaneous symptoms from 2006 to 2020 in Spain. EV-positive samples from 368 patients were included. EV species A were identified in 85.1% of those typed EV. Coxsackievirus (CV) A6 was the prevalent serotype (60.9%), followed by EV-A71 (9.9%) and CVA16 (7.7%). Infections affected children (1–6 years old) mainly, and show seasonality with peaks in spring–summer and autumn. Clinical data indicated few cases of atypical HFMD as well as those with neurological complications (associated with the 2016 EV-A71 outbreak). Phylogenetic analysis of CVA6 VP1 sequences showed different sub-clusters circulating from 2010 to present. In conclusion, HFMD or exanthemas case reporting has increased in Spain in recent years, probably associated with an increase in circulation of CVA6, although they did not seem to show greater severity. However, EV surveillance in mucocutaneous manifestations should be improved to identify the emergence of new types or variants causing outbreaks and more severe pathologies.
Plant Feed Additives as Natural Alternatives to the Use of Synthetic Antioxidant Vitamins on Poultry Performances, Health, and Oxidative Status: A Review of the Literature in the Last 20 Years

Plant feed additives (PFA) such as essential oils, extracts, and by-products from plant processing can be included in poultry diets. A total of 39 peer-reviewed articles were selected from the literature published in the last 20 years (2000–2020) comparing PFA antioxidant effects with synthetic antioxidant vitamins (mainly vitamin E) in poultry nutrition. The PFA can be used as an effective nutritional strategy to face poultry’s oxidative stress with positive impact also on their productivity and efficiency. They can partially or completely replace antioxidant synthetic vitamins (the latter administered at doses between 150 and 500 mg/kg) in animal diets, sometimes affecting important physiological functions or expressing synergistic effect with the synthetic antioxidants. It is crucial to take into consideration the issues related to the absorption and the metabolism of these additives and their interaction with gut microbiota. However, some form- and dose-dependent negative effects on growth performances are observed.
SOD3 Is a Non-Mutagenic Growth Regulator Affecting Cell Migration and Proliferation Signal Transduction

Superoxide dismutase (SOD) family isoenzymes, SOD1, SOD2, and SOD3, synthesize hydrogen peroxide (H2O2), which regulates the signal transduction. H2O2 is a second messenger able to enter into the cells through aquaporin 3 cell membrane channels and to modify protein tyrosine phosphatase activity. SOD3 has been shown to activate signaling pathways in tissue injuries, inflammation, and cancer models. Similar to the H2O2 response in the cells, the cellular response of SOD3 is dose-dependent; even a short supraphysiological concentration reduces the cell survival and activates the growth arrest and apoptotic signaling, whereas the physiological SOD3 levels support its growth and survival. In the current work, we studied the signaling networks stimulated by SOD3 overexpression demonstrating a high diversity in the activation of signaling cascades. The results obtained suggest that SOD3, although inducing cell growth and affecting various biological processes, does not cause detectable long-term DNA aberrations. Therefore, according to the present data, SOD3 is not a mutagen. Additionally, we compared SOD3-driven immortalized mouse embryonic fibroblasts to SV40 immortalized NIH3T3 cells, demonstrating a marked difference in the activation of cellular kinases. The data presented may contain important druggable targets to abrogate unwanted cell growth.
Assessment of Bioactive Compounds under Simulated Gastrointestinal Digestion of Bee Pollen and Bee Bread: Bioaccessibility and Antioxidant Activity

Bee pollen and bee bread have always been regarded as excellent natural resources for application in food and pharmaceutical fields due to their rich nutrient content and diversity of bioactive compounds with health-improving properties. Extensive studies on both bee products as ingredients for a healthy diet were reported, although the data concerning their metabolization on the gastrointestinal tract is quite limited. Here, we report, at each digestive stage, the bioactive profile for both bee products, their bioaccessibility levels and the antioxidant activity evaluation. The findings indicated that the average bioaccessibility level of total phenolic and total flavonoid content for bee pollen was 31% and 25%, respectively, while it was 38% and 35% for bee bread. This was reflected in a decrease of their antioxidant capacity at the end of in vitro gastrointestinal digestion, both in free radicals scavenging capacity and in reducing power. Moreover, within the 35 phytochemicals identified, the most affected by gastrointestinal digestion were phenylamides, with a complete digestibility at the end of the intestinal phase. Overall, our results highlight that bioactive compounds in both raw products do not reflect the real amount absorbed in the intestine, being bee bread more accessible in bioactive content than bee pollen.
Evaluation of Non-Uniform Image Quality Caused by Anode Heel Effect in Digital Radiography Using Mutual Information

Anode heel effects are known to cause non-uniform image quality, but no method has been proposed to evaluate the non-uniform image quality caused by the heel effect. Therefore, the purpose of this study was to evaluate non-uniform image quality in digital radiographs using a novel circular step-wedge (CSW) phantom and normalized mutual information (nMI). All X-ray images were acquired from a digital radiography system equipped with a CsI flat panel detector. A new acrylic CSW phantom was imaged ten times at various kVp and mAs to evaluate overall and non-uniform image quality with nMI metrics. For comparisons, a conventional contrast-detail resolution phantom was imaged ten times at identical exposure parameters to evaluate overall image quality with visible ratio (VR) metrics, and the phantom was placed in different orientations to assess non-uniform image quality. In addition, heel effect correction (HEC) was executed to elucidate the impact of its effect on image quality. The results showed that both nMI and VR metrics significantly changed with kVp and mAs, and had a significant positive correlation. The positive correlation is suggestive that the nMI metrics have a similar performance to the VR metrics in assessing the overall image quality of digital radiographs. The nMI metrics significantly changed with orientations and also significantly increased after HEC in the anode direction. However, the VR metrics did not change significantly with orientations or with HEC. The results indicate that the nMI metrics were more sensitive than the VR metrics with regards to non-uniform image quality caused by the anode heel effect. In conclusion, the proposed nMI metrics with a CSW phantom outperformed the conventional VR metrics in detecting non-uniform image quality caused by the heel effect, and thus are suitable for quantitatively evaluating non-uniform image quality in digital radiographs with and without HEC.
A Novel, Inexpensive In-House Immunochromatographic Strip Test for Cryptococcosis Based on the Cryptococcal Glucuronoxylomannan Specific Monoclonal Antibody 18B7

The aim of this study was to develop a novel lateral flow immunochromatoghaphic strip test (ICT) for detecting cryptococcal polysaccharide capsular antigens using only a single specific monoclonal antibody, mAb 18B7. The mAb 18B7 is a well characterized antibody that specifically binds repeating epitopes displayed on the cryptococcal polysaccharide glucuronoxylomannan (GXM). We validated the immunoreactivities of mAb 18B7 against capsular antigens of different cryptococcal serotypes. The mAb 18B7 ICT was constructed as a sandwich ICT strip and the antibody serving in the mobile phase (colloidal gold conjugated mAb 18B7) to bind one of the GXM epitopes while the stationary phase antibody (immobilized mAb18B7 on test line) binding to other remaining unoccupied epitopes to generate a positive visual readout. The lower limit of detection of capsular antigens for each of the Cryptococcus serotypes tested was 0.63 ng/mL. No cross-reaction was found against a panel of antigens isolated from cultures of other pathogenic fungal, except the crude antigen of Trichosporon sp. with the lower limit of detection of 500 ng/mL (~800 times higher than that for cryptococcal GXM). The performance of the mAb 18B7 ICT strip was studied using cerebrospinal fluid (CSF) and serum and compared to commercial diagnostic kits (latex agglutination CALAS and CrAg IMMY). The sensitivity, specificity and accuracy of the mAb18B7 ICT with CSF from patients with confirmed cryptococcal meningitis were 92.86%, 100% and 96.23%, respectively. No false positives were observed with samples from non-cryptococcosis patients. With serum samples, the mAb 18B7 ICT gave a sensitivity, specificity and accuracy of 96.15%, 97.78% and 96.91%, respectively. Our results show that the mAb 18B7 based ICT was reliable, reproducible, and cost-effective as a point-of-care immunodiagnostic test for cryptococcosis. The mAb 18B7 ICT may be particularly useful in countries where commercial kits are not available or affordable.
Combined powder X-ray diffraction data and quantum-chemical calculations in EXPO2014

This paper describes new features implemented in the EXPO2014 software and aimed at assisting crystallographers in the use of quantum-chemistry calculations in combination with experimental powder diffraction data. The implemented tools are useful in particular in two important steps of the process of crystal structure determination from powder diffraction data: (1) preparing accurate structural model suitable for crystal structure determination by real-space methods; (2) validating structure determination. The combination of experimental/quantum-chemical methods in EXPO2014 is now managed easily thanks to the following capabilities: (a) converting crystallographic data in input files and reading molecular geometry from output files of a wide variety of computational chemistry packages (GAMESS-US, NWChem, Gaussian, CRYSTAL, ABINIT, QUANTUM ESPRESSO); (b) optimizing the geometry of a molecule using Open Babel's force fields; (c) a graphical interface to run semi-empirical quantum calculation by MOPAC (Molecular Orbital PACkage); (d) producing input file for dispersion-corrected density functional theory.