Miracle-dz/UniFAR-FTUs huggingface dataset:
Method for the Production and Purification of Plant Immuno-Active Xylanase from Trichoderma

Plants lack a circulating adaptive immune system to protect themselves against pathogens. Therefore, they have evolved an innate immune system based upon complicated and efficient defense mechanisms, either constitutive or inducible. Plant defense responses are triggered by elicitors such as microbe-associated molecular patterns (MAMPs). These components are recognized by pattern recognition receptors (PRRs) which include plant cell surface receptors. Upon recognition, PRRs trigger pattern-triggered immunity (PTI). Ethylene Inducing Xylanase (EIX) is a fungal MAMP protein from the plant-growth-promoting fungi (PGPF)–Trichoderma. It elicits plant defense responses in tobacco (Nicotiana tabacum) and tomato (Solanum lycopersicum), making it an excellent tool in the studies of plant immunity. Xylanases such as EIX are hydrolytic enzymes that act on xylan in hemicellulose. There are two types of xylanases: the endo-1, 4-β-xylanases that hydrolyze within the xylan structure, and the β-d-xylosidases that hydrolyze the ends of the xylan chain. Xylanases are mainly synthesized by fungi and bacteria. Filamentous fungi produce xylanases in high amounts and secrete them in liquid cultures, making them an ideal system for xylanase purification. Here, we describe a method for cost- and yield-effective xylanase production from Trichoderma using wheat bran as a growth substrate. Xylanase produced by this method possessed xylanase activity and immunogenic activity, effectively inducing a hypersensitive response, ethylene biosynthesis, and ROS burst.
Classification of Skin Disease Using Deep Learning Neural Networks with MobileNet V2 and LSTM

Deep learning models are efficient in learning the features that assist in understanding complex patterns precisely. This study proposed a computerized process of classifying skin disease through deep learning based MobileNet V2 and Long Short Term Memory (LSTM). The MobileNet V2 model proved to be efficient with a better accuracy that can work on lightweight computational devices. The proposed model is efficient in maintaining stateful information for precise predictions. A grey-level co-occurrence matrix is used for assessing the progress of diseased growth. The performance has been compared against other state-of-the-art models such as Fine-Tuned Neural Networks (FTNN), Convolutional Neural Network (CNN), Very Deep Convolutional Networks for Large-Scale Image Recognition developed by Visual Geometry Group (VGG), and convolutional neural network architecture that expanded with few changes. The HAM10000 dataset is used and the proposed method has outperformed other methods with more than 85% accuracy. Its robustness in recognizing the affected region much faster with almost 2× lesser computations than the conventional MobileNet model results in minimal computational efforts. Furthermore, a mobile application is designed for instant and proper action. It helps the patient and dermatologists identify the type of disease from the affected region’s image at the initial stage of the skin disease. These findings suggest that the proposed system can help general practitioners efficiently and effectively diagnose skin conditions, thereby reducing further complications and morbidity.
The p23 of Citrus Tristeza Virus Interacts with Host FKBP-Type Peptidyl-Prolylcis-Trans Isomerase 17-2 and Is Involved in the Intracellular Movement of the Viral Coat Protein

Citrus tristeza virus is a member of the genus Closterovirus in the family Closteroviridae. The p23 of citrus tristeza virus (CTV) is a multifunctional protein and RNA silencing suppressor. In this study, we identified a p23 interacting partner, FK506-binding protein (FKBP) 17-2, from Citrus aurantifolia (CaFKBP17-2), a susceptible host, and Nicotiana benthamiana (NbFKBP17-2), an experimental host for CTV. The interaction of p23 with CaFKBP17-2 and NbFKBP17-2 were individually confirmed by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Subcellular localization tests showed that the viral p23 translocated FKBP17-2 from chloroplasts to the plasmodesmata of epidermal cells of N. benthamiana leaves. The knocked-down expression level of NbFKBP17-2 mRNA resulted in a decreased CTV titer in N. benthamiana plants. Further, BiFC and Y2H assays showed that NbFKBP17-2 also interacted with the coat protein (CP) of CTV, and the complexes of CP/NbFKBP17-2 rapidly moved in the cytoplasm. Moreover, p23 guided the CP/NbFKBP17-2 complexes to move along the cell wall. To the best of our knowledge, this is the first report of viral proteins interacting with FKBP17-2 encoded by plants. Our results provide insights for further revealing the mechanism of the CTV CP protein movement.
Heterostructural Mixed Oxides Prepared via ZnAlLa LDH or ex-ZnAl LDH Precursors—Effect of La Content and Its Incorporation Route

The effect of La content and its incorporation route on physicochemical properties of ZnO/Zn(Al,La)2O4 or La2O3–ZnO/ZnAl2O4 mixed oxides with a spinel structure obtained from ZnAlLa Layered double hydroxides (LDHs) or ex-ZnAl LDH materials was investigated. The heterostructural nanocomposites with the similar Zn/Al molar ratio and varied La content were prepared by two techniques: via co-precipitation and thermal treatment of ZnAlLa LDHs at 500 °C or via incipient wetness impregnation of ex-ZnAl LDHs with aqueous solutions of lanthanum nitrate and subsequent thermal treatment. The obtained series of materials were characterized by the following techniques: X-ray fluorescence (XRF), N2 adsorption (BET), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), thermogravimetric analysis with evolved gas analysis (TG/DTG/EGA), scanning transmission electron microscopy (STEM) energy-dispersive X-ray spectroscopy (EDS), high-resolution transmission electron microscopy (HRTEM) and Fourier-transform infrared spectroscopy (FFT). The evaluation of activity toward the high-temperature water gas shift (HT-WGS) within the temperature range of 350–420 °C was carried out on the basis of rate constant measurements in the kinetic mode using a differential reactor. The co-precipitation technique allowed for a better distribution of La in bulk and on the spinel surface than in case of lanthanum incorporation via impregnation. ZnO/Zn(Al,La)2O4 or La2O3–ZnO/ZnAl2O4 mixed oxides were characterized by moderate activity in the HT-WGS reaction. The results reveal that introduction of lanthanum oxide over 2.4–2.8 wt% induces the phase separation of the ZnAl2O4 spinel, forming ZnO on the ZnAl2O4 spinel surface.
Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men

(1) Background: Aging is associated with a progressive decline in muscle mass and function. Aging is also a primary risk factor for metabolic syndrome, which further alters muscle metabolism. However, the molecular mechanisms involved remain to be clarified. Herein we performed omic profiling to decipher in muscle which dominating processes are associated with healthy aging and metabolic syndrome in old men. (2) Methods: This study included 15 healthy young, 15 healthy old, and 9 old men with metabolic syndrome. Old men were selected from a well-characterized cohort, and each vastus lateralis biopsy was used to combine global transcriptomic and proteomic analyses. (3) Results: Over-representation analysis of differentially expressed genes (ORA) and functional class scoring of pathways (FCS) indicated that healthy aging was mainly associated with upregulations of apoptosis and immune function and downregulations of glycolysis and protein catabolism. ORA and FCS indicated that with metabolic syndrome the dominating biological processes were upregulation of proteolysis and downregulation of oxidative phosphorylation. Proteomic profiling matched 586 muscle proteins between individuals. The proteome of healthy aging revealed modifications consistent with a fast-to-slow transition and downregulation of glycolysis. These transitions were reduced with metabolic syndrome, which was more associated with alterations in NADH/NAD+ shuttle and β-oxidation. Proteomic profiling further showed that all old muscles overexpressed protein chaperones to preserve proteostasis and myofiber integrity. There was also evidence of aging-related increases in reactive oxygen species but better detoxifications of cytotoxic aldehydes and membrane protection in healthy than in metabolic syndrome muscles. (4) Conclusions: Most candidate proteins and mRNAs identified herein constitute putative muscle biomarkers of healthy aging and metabolic syndrome in old men.
Citric Acid Cycle Metabolites Predict Infarct Size in Pigs Submitted to Transient Coronary Artery Occlusion and Treated with Succinate Dehydrogenase Inhibitors or Remote Ischemic Perconditioning

Succinate dehydrogenase (SDH) inhibition with malonate during reperfusion reduced myocardial infarction in animals, whereas its endogenous substrate, succinate, is detected in plasma from STEMI patients. We investigated whether protection by SDH inhibition is additive to that of remote ischemic perconditioning (RIC) in pigs submitted to transient coronary artery occlusion, and whether protective maneuvers influence plasma levels of citric acid cycle metabolites. Forty pigs were submitted to 40 min coronary occlusion and reperfusion, and allocated to four groups (controls, sodium malonate 10 mmol/L, RIC, and malonate + RIC). Plasma was obtained from femoral and great cardiac veins and analyzed by LC-MS/MS. Malonate, RIC, and malonate + RIC reduced infarct size (24.67 ± 5.98, 25.29 ± 3.92 and 29.83 ± 4.62% vs. 46.47 ± 4.49% in controls, p < 0.05), but no additive effects were detected. Enhanced concentrations of succinate, fumarate, malate and citrate were observed in controls during initial reperfusion in the great cardiac vein, and most were reduced by cardioprotective maneuvers. Concentrations of succinate, fumarate, and malate significantly correlated with infarct size. In conclusion, despite the combination of SDH inhibition during reperfusion and RIC did not result in additive protection, plasma concentrations of selected citric acid cycle metabolites are attenuated by protective maneuvers, correlate with irreversible injury, and might become a prognosis tool in STEMI patients.
Evaluation of Sex Differences in Murine Diabetic Ketoacidosis and Neutropenic Models of Invasive Mucormycosis

There is increased concern that the quality, generalizability and reproducibility of biomedical research can be influenced by the sex of animals used. We studied the differences between male and female mice in response to invasive pulmonary mucormycosis including susceptibility to infection, host immune reaction and responses to antifungal therapy. We used diabetic ketoacidotic (DKA) or neutropenic mice infected with either Rhizopus delemar or Mucor circinelloides. The only difference detected was that when DKA mice were infected with M. circinelloides, female mice were more resistant to infection than male mice (median survival time of 5 vs. 2 days for female and male mice, respectively). However, a 100% lethality was detected among infected animals of both sexes. Treatment with either liposomal amphotericin B (L-AMB) or posaconazole (POSA) protected mice from infection and eliminated the difference seen between infected but untreated female and male mice. Treatment with L-AMB consistently outperformed POSA in prolonging survival and reducing tissue fungal burden of DKA and neutropenic mice infected with R. delemar or M. circinelloides, in both mouse sexes. While little difference was detected in cytokine levels among both sexes, mucormycosis infection in the DKA mouse model induced more inflammatory cytokines/chemokines involved in neutrophil (CXCL1) and macrophage (CXCL2) recruitment vs. uninfected mice. As expected, this inflammatory response was reduced in the neutropenic mouse model. Our studies show that there are few differences between female and male DKA or neutropenic mice infected with mucormycosis with no effect on the outcome of treatment or host immune response.
When the COVID-19 Pandemic Surges during Influenza Season: Lessons Learnt from the Sentinel Laboratory-Based Surveillance of Influenza-Like Illness in Lombardy during the 2019–2020 Season

This paper outlines the role of Lombardy’s regional influenza reference laboratory (Northern Italy) in the surveillance of influenza-like illnesses (ILIs) in monitoring SARS-CoV-2 circulation by analyzing 631 consecutive nasopharyngeal swabs (NPSs) collected from ILI outpatients by sentinel physicians during the 2019–2020 season. The samples were tested by specific real-time RT-PCRs targeting SARS-CoV-2, influenza viruses, and RSVs. Results: Of these NPSs, 31% tested positive for influenza viruses, 10% for SARS-CoV-2, and 7% for RSV. No coinfections were detected. Influenza viruses and RSVs circulated throughout the surveillance period until the end of February (week 9-2020), when they suddenly ceased to circulate seven weeks earlier than during the previous five influenza seasons. After the first detection of SARS-CoV-2 in our ILI outpatients at the beginning of March (week 10-2020), SARS-CoV-2 remained the only virus identified throughout the surveillance period. Patients ≥ 65 years had a 3.2-fold greater risk of being infected with SARS-CoV-2, while school-age children (5–14 years) and children < 5 years proved to be the age groups most at risk of contracting influenza viruses and RSV, respectively. Our experience demonstrates that laboratory-based ILI surveillance networks are essential for identifying SARS-CoV-2 cases that would otherwise remain undetected, in order to stop their spread within our communities.
Clinical Characteristics of Primary Repair for Perforated Peptic Ulcer: 10-Year Experience in a Single Center

Background: Perforated peptic ulcer (PPU) is a disease whose incidence is decreasing. However, PPU still requires emergency surgery. The aim of this study was to review the clinical characteristics of patients who received primary repair for PPU and identify the predisposing factors associated with severe complications. Method: From January 2011 to December 2020, a total of 75 patients underwent primary repair for PPU in our hospital. We reviewed the patients’ data, including general characteristics and perioperative complications. Surgical complications were evaluated using the Clavien-Dindo Classification (CDC) system, with which we classified patients into the mild complication (CDC 0–III, n = 61) and severe complication (CDC IV–V, n = 14) groups. Result: Fifty patients had gastric perforation, and twenty-five patients had duodenal perforation. Among surgical complications, leakage or fistula were the most common (5/75, 6.7%), followed by wound problems (4/75, 5.3%). Of the medical complications, infection (9/75, 12%) and pulmonary disorder (7/75, 9.3%) were common. Eight patients died within thirty days after surgery (8/75, 10.7%). Liver cirrhosis was the most significant predisposing factor for severe complications (HR = 44.392, p = 0.003). Conclusion: PPU is still a surgically important disease that has significant mortality, above 10%. Liver cirrhosis is the most important underlying disease associated with severe complications.
Intelligent Diagnosis of Thyroid Ultrasound Imaging Using an Ensemble of Deep Learning Methods

Background and Objectives: At present, thyroid disorders have a great incidence in the worldwide population, so the development of alternative methods for improving the diagnosis process is necessary. Materials and Methods: For this purpose, we developed an ensemble method that fused two deep learning models, one based on convolutional neural network and the other based on transfer learning. For the first model, called 5-CNN, we developed an efficient end-to-end trained model with five convolutional layers, while for the second model, the pre-trained VGG-19 architecture was repurposed, optimized and trained. We trained and validated our models using a dataset of ultrasound images consisting of four types of thyroidal images: autoimmune, nodular, micro-nodular, and normal. Results: Excellent results were obtained by the ensemble CNN-VGG method, which outperformed the 5-CNN and VGG-19 models: 97.35% for the overall test accuracy with an overall specificity of 98.43%, sensitivity of 95.75%, positive and negative predictive value of 95.41%, and 98.05%. The micro average areas under each receiver operating characteristic curves was 0.96. The results were also validated by two physicians: an endocrinologist and a pediatrician. Conclusions: We proposed a new deep learning study for classifying ultrasound thyroidal images to assist physicians in the diagnosis process.
Polyphenol Profiling of Chestnut Pericarp, Integument and Curing Water Extracts to Qualify These Food By-Products as a Source of Antioxidants

Plant polyphenols have beneficial antioxidant effects on human health; practices aimed at preserving their content in foods and/or reusing food by-products are encouraged. The impact of the traditional practice of the water curing procedure of chestnuts, which prevents insect/mould damage during storage, was studied to assess the release of polyphenols from the fruit. Metabolites extracted from pericarp and integument tissues or released in the medium from the water curing process were analyzed by matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electrospray-quadrupole-time of flight-mass spectrometry (ESI-qTOF-MS). This identified: (i) condensed and hydrolyzable tannins made of (epi)catechin (procyanidins) and acid ellagic units in pericarp tissues; (ii) polyphenols made of gallocatechin and catechin units condensed with gallate (prodelphinidins) in integument counterparts; (iii) metabolites resembling those reported above in the wastewater from the chestnut curing process. Comparative experiments were also performed on aqueous media recovered from fruits treated with processes involving: (i) tap water; (ii) tap water containing an antifungal Lb. pentosus strain; (iii) wastewater from a previous curing treatment. These analyses indicated that the former treatment determines a 6–7-fold higher release of polyphenols in the curing water with respect to the other ones. This event has a negative impact on the luster of treated fruits but qualifies the corresponding wastes as a source of antioxidants. Such a phenomenon does not occur in wastewater from the other curing processes, where the release of polyphenols was reduced, thus preserving the chestnut’s appearance. Polyphenol profiling measurements demonstrated that bacterial presence in water hampered the release of pericarp metabolites. This study provides a rationale to traditional processing practices on fruit appearance and qualifies the corresponding wastes as a source of bioactive compounds for other nutraceutical applications.
PKM2 regulates proliferation and apoptosis through the Hippo pathway in oral tongue squamous cell carcinoma

Oral tongue squamous cell carcinoma (OTSCC) is a highly malignant type of tumor. The 5-year survival rate of patients with advanced tongue squamous cell carcinoma is only ~50%. Pyruvate kinase M2 (PKM2) is the key rate-limiting enzyme of glycolysis, maintaining the Warburg effect in tumor cells. The present study aimed to investigate the relationship between PKM2 expression and the poor prognosis of patients with OTSCC and to determine oral squamous carcinoma tumor cell proliferation and apoptosis. Reverse transcription-quantitative (RT-q) PCR, western blotting and immunohistochemistry were used to analyze the expression levels of PKM2 in OTSCC, and the clinicopathological characteristics and prognosis of patients with OTSCC were further analyzed by statistical analysis. The results from RT-qPCR and immunohistochemistry demonstrated that PKM2 was upregulated in OTSCC tissues and highly expressed in advanced stage OTSCC tissues compared with paired adjacent tissues and lower stage OTSCC tissues. Patients with OTSCC and high PKM2 expression had shorter overall survival (OS) compared with those with low PKM2 expression. Furthermore, high expression of PKM2 was significantly associated with Tumor-Node-Metastasis (TNM) stage. TNM stage and PKM2 expression were independent predictive factors for OS in patients with OTSCC. In addition, PKM2 knockdown inhibited the proliferation and increased the apoptosis of oral squamous carcinoma tumor cells. Furthermore, PKM2 knockdown could regulate the expression of cell cycle and apoptosis-related proteins by activating Hippo signaling pathway, as confirmed by the decreased expression of yes-associated protein 1 (YAP), Bcl-2 and Ki-67 and the increased expression of large tumor suppressor kinase 1, phosphorylated YAP and Bax. Taken together, the findings from this study demonstrated that PKM2 may be considered as a potential target for the diagnosis and treatment of OTSCC.
Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales

Mucorales are the causal agents for the lethal disease known as mucormycosis. Mortality rates of mucormycosis can reach up to 90%, due to the mucoralean antifungal drug resistance and the lack of effective therapies. A concerning urgency among the medical and scientific community claims to find targets for the development of new treatments. Here, we reviewed different studies describing the role and machinery of a novel non-canonical RNAi pathway (NCRIP) only conserved in Mucorales. Its non-canonical features are the independence of Dicer and Argonaute proteins. Conversely, NCRIP relies on RNA-dependent RNA Polymerases (RdRP) and an atypical ribonuclease III (RNase III). NCRIP regulates the expression of mRNAs by degrading them in a specific manner. Its mechanism binds dsRNA but only cuts ssRNA. NCRIP exhibits a diversity of functional roles. It represses the epimutational pathway and the lack of NCRIP increases the generation of drug resistant strains. NCRIP also regulates the control of retrotransposons expression, playing an essential role in genome stability. Finally, NCRIP regulates the response during phagocytosis, affecting the multifactorial process of virulence. These critical NCRIP roles in virulence and antifungal drug resistance, along with its exclusive presence in Mucorales, mark this pathway as a promising target to fight against mucormycosis.
Studies on cancrinites; Part 2, Stability fields and cell dimensions of calcium and potassium-rich cancrinites

Cancrinites of compositions 3NaAlSiO 4 XCaCO 3 ,3NaAlSiO 4 XCa(OH) 2 and 3NaAlSiO 4 XK 2 O 3 were made in the 200 degrees to 800 degrees C range at 10,000 to 30,000 psi of water pressure. The first two compositions did not dissociate at upper pressure and temperature limits but the third composition dissociated to nepheline and probably K 2 CO 3 at 425-475 degrees C. Synthetic 3NaAlSiO 4 XNa 2 CO 3 , 3NaAlSiO 4 XNaHCO 3 , and 3NaAlSiO 4 XKHCO 3 cancrinites were made also. Cell edges (+ or -0.02 A) for the six compositions given above and in the same order are: a=12.59, 12.60, 12.73, 12.67, 12.67, 12.73, and c=5.17, 5.14, 5.18, 5.18, 5.16, 5.20 with Vol. (A) - 710, 707, 727, 717, 728. Analcite and a carbonate or hydroxide appeared at low temperatures with cancrinite. Cell edges for four unanalysed natural specimens are given.