Miracle-dz/UniFAR-FTUs huggingface dataset:
Epithelial cell death induced by Candidalysin, a cytolytic peptide toxin of Candida albicans

2 Acknowledgements . 3 Table of contents . 4 List of Figures . 9 List of Tables . 13 List of Abbreviations . 14 Chapter 1: Introduction. 19 1.1 Host-Pathogen interaction . 19 1.2 Candida species . 20 1.3 Candida infections . 21 1.3. 1 Treatment of Candida infections . 22 1.4 Candida albicans virulence factors . 23 1.4. 1 Hyphae . 24 1.4. 2 C. albicans virulence factors . 26 1.4. 3 Adhesion. 26 1.4. 4 Invasion . 27 1.4. 5 Damage . 30 1.5 Physical barrier against C. albicans infection . 30 1.6 Host immune responses against C. albicans infection. 31 1.6. 1 Host recognition of microbes . 31 1.6. 2 Innate responses to C. albicans . 33 1.6. 3 Adaptive responses to C. albicans . 37 1.7 Host cell death as a defence against infection . 38 1.7. 1 The interplay between apoptosis and necrosis . 40 1.7. 2 Apoptosis . 42 1.7. 3 Necrosis . 48 5 1.7. 4 Programmed necrosis . 48 1.7. 5 Summary of the characteristic features of different cell death pathways . 57 1.8 Project Aims . 59 Chapter 2: Materials and Methods . 60 2.1 General materials and equipment . 60 2.1.1 General chemicals . 60 2.1.2 General equipment . 61 2.2 Fungal culture . 61 2.2.1 C. albicans growth medium . 61 2.2.2 Creation of C. albicans mutants, growth and maintenance . 61 2.2.3 Candidalysin peptides . 63 2.3 Cell culture . 63 2.3. 1 Cell line growth and maintenance . 63 2.3. 2 Cell counting . 64 2.3. 3 Cell freezing and thawing . 64 2.3. 4 Cell seeding . 65 2.4 Cell response assays . 66 2.4. 1 LDH (Epithelial cell damage) assay . 66 2.4. 2 Detection of epithelial cell death by fluorescence microscopy . 66 2.4. 3 Measurement of epithelial mitochondrial fitness by MTT assay . 67 2.4. 4 Intracellular ROS quantification by DCFH-DA staining . 67 2.4. 5 Intracellular ATP quantification by Luminescence assay . 68 2.4. 6 Intracellular calcium quantification by fura-2 staining . 68 2.4. 7 Caspase activity measurement by Luminescence assay . 68 2.4. 8 Cytochrome c and Cytokine quantification by ELISA assay . 69 2.5 Protein assays . 69 2.5. 1 Protein extraction . 69 2.5. 2 Bicinchoninic Acid (BCA) assay . 69 2.5. 3 Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) . 70 2.5. 4 Western blot analysis . 70
Isotopic Constraints on the Atmospheric Sources and Formation of
Nitrogenous Species in Biomass-Burning-Influenced Clouds

Abstract. The interpretation of tropospheric cloud formation rests on understanding the sources and processes affecting aerosol constituents of the atmosphere that are preserved in cloudwater. However, this challenge is difficult to be quantitatively addressed based on the sole use of bulk chemical properties. Nitrogenous aerosols, mainly ammonium (NH4+) and nitrate (NO3−), play an important role in tropospheric cloud formation. Here we collected cloudwater samples at the summit of Mt. Tai (1545 m above sea level) in Eastern China during a long-lasting biomass burning (BB) event, and measured for the first time the isotopic compositions (mean ± 1σ) of cloudwater nitrogen species (δ15N-NH4+ = −6.53 ± 4.96 ‰, δ15N-NO3− = −2.35 ± 2.00 ‰, δ18O-NO3− = 57.80 ± 4.23 ‰), allowing insights into their sources and potential transformation mechanism within the clouds. Large contributions of BB to the cloudwater NH4+ (32.9 ± 4.6 %) and NO3− (28.2 ± 2.7 %) inventories were confirmed through a Bayesian isotopic mixing model, coupled with our newly-developed computational quantum chemistry module. Despite an overall reduction in total anthropogenic NOx emission due to effective emission control actions and stricter emission standards for vehicles, the observed cloud δ15N-NO3− values suggest that NOx emissions from transportation may have exceeded emissions from coal combustion. δ18O-NO3− values imply that the reaction of OH with NO2 is the dominant pathway of NO3− formation (57 ± 11 %), yet the contribution of heterogeneous hydrolysis of dinitrogen pentoxide was almost as important (43 ± 11 %).
Evaluate the Performance of Fenton Process for the Removal of Methylene Blue from Aqueous Solution: Experimental, Neural Network Modeling and Optimization

In this article, degradation of Methylene Blue by Fenton's oxidation process was investigated. The effect of, Fe2+ and H2O2 concentrations and reaction time in initial concentration of the dye = 10 mg/L, pH = 3 and lab temperature on the dye removal was studied. Also, Artificial Neural Networks (ANN) was applied to model the dye removal data obtained by Fenton oxidation process. A network consisting of two layers of eight neurons in the hidden layer was considered. Very low root mean squared error (RMSE) of 1.262 and high determination of coefficient (R2) of 0.995 in the network calculation verified validity of the acquired network for further analysis and optimization. © 2018 American Institute of Chemical Engineers Environ Prog, 39:e13126, 2020
Phytochemicals of lentil (Lens culinaris) and their antioxidant and anti-inflammatory effects

Lentils contain a plethora of bioactive phytochemicals such as extractable and insoluble-bound phenolics, carotenoids, tocopherols, saponins, phytic acid, and phytosterols, which have been increasingly attributed to the health benefits of lentil consumption in the diet. The concentration and stability of these phytochemicals in lentils may be affected by several processing parameters including different thermal processing, exogenous enzyme treatment and germination. Consumption of lentils has been associated with the risk reduction of many diseases due to the potential antioxidant activity and anti-inflammatory potential of phytochemicals in lentils. This mini review is intended to provide most current information on the phytochemical composition of lentils, and the potential antioxidant and anti-inflammatory properties of these compounds.
DESIGN, DEVELOPMENT, AND CHARACTERIZATION OF TOPICAL GEL CONTAINING ITRACONAZOLE - ANTIFUNGAL AGENT

Objective: The main purpose of this study was to develop a topical delivery of itraconazole to reduce the dose of the drug, to improve patient compliance, and to avoid the side effects. Itraconazole is a triazole derivative to treat antifungal and antiprotozoal infections. Methods: Topical gel formulations of itraconazole were prepared using Carbopol 940 as a gelling agent with different concentrations. Four different formulations were prepared and evaluated with respect to color, spreadability, viscosity measurement, determination of pH, drug content, in vitro drug release studies, zeta potential studies, and stability studies. Compatibility study was carried out by Fourier-transform infrared (FT-IR) spectral analysis. Results: FT-IR study revealed that there were no significant interaction between the drug and polymers. All the prepared formulations show acceptable physical properties. The drug content and percentage yield were higher for F1 formulation among all formulation F1 shows better drug release. Stability study of best formulation shows that there was no difference in drug content and in vitro drug release studies. Conclusion: From the above observation results that this formulation may be more encouraging topical substitute for the healing of fungal infections in the skin.
Nitrogen Rate and Cutting Management for Fenugreek Green Leaf and Seed Production

Fenugreek (Trigonella foenum-graecum L.) is an annual seed spice crop also used as a leafy vegetable, and reported to have medicinal properties. Farmers usually practice leaf cutting in fenugreek only when crop grown for vegetable purpose. There is need to standardize the nitrogen requirement when leaf cutting is practiced at different stages of growth since it may influence leaf and seed yields. Hence, present field Experiment was conducted to study the effect of Nitrogen rate and Cutting Management on Fenugreek leaf and seed production during 15th November, 2015 to 25th March, 2016. Treatments were comprised of three nitrogen levels of 20, 40 or 60 kg ha-1 and three levels of cutting i.e. no cutting, or cutting at 45 or 60 days after sowing (DAS). All treatment combinations were replicated 3 times in a factorial randomized complete block design. The observations were recorded on plant height, number of pods plant-1, number of seed pod-1, green leaf yield, seed yield and biological yield (sum of seed and straw yield). Harvest index was calculated by dividing economic yield to biological yield. The results revealed that increased green leaf and seed yields occurred when nitrogen level increased and cutting was delayed. The maximum harvest index (0.44) was when nitrogen was applied @ 60 kg ha-1 and plants were cut at 60 DAS. Thus, delaying cutting increases nitrogen requirement in fenugreek if supplied in proper amount, it results to increased yield.
Electrospun silk fibroin/β-cyclodextrin citrate nanofibers as a novel biomaterial for application in controlled drug release

Abstract A novel β-cyclodextrin-grafted silk fibroin (SF) nanofibers was successfully fabricated. The morphology and diameter of the electrospun nanofibers were characterized. FE-SEM images showed that the morphology and diameter of the nanofibers were mainly affected by weight ratio of the blend. FTIR, 1H-NMR, DSC and TGA confirmed the crosslinking reaction between β-cyclodextrin and SF. The release rate of Ciprofloxacin was measured and observed that the SF-g-CD nanofibrous mat provided slower release of the entrapped drug when compared with SF nanofibrous mat. A mathematical analysis of the drug release data suggested that the Higuchi model was the best fitted model. Graphical Abstract
Analysis of B and T cell intracellular signaling pathway activation in Selective IgA deficiency

5 Acknowledgements . 8 Table of contents . 9 List of figures . 11 List of tables . 12 List of abbreviations . 13 1 Background . 15 1.1 The immune system . 15 1.2 The innate immune system . 15 1.3 Adaptive immune system . 16 1.3.1 B cells . 16 1.3.2 T cells . 17 1.4 Immunoglobulin A . 18 1.5 SIgAD . 18 1.6 Causes of SIgAD and genetic factors . 19 1.7 Signaling pathways . 20 1.7. 1 Jak-STAT . 20 1.7. 2 MAPKs . 21 1.8 Phosphoflow cytometry – observing immune responses . 22 1.8. 1 Advantages of Phosphoflow . 23 1.8. 2 Staining protocols . 24 1.8. 3 Limitations . 24 1.8. 4 Phosphoflow cytometry – clinical relevance . 25 2 Aims of the study . 26 2.1 General aims . 26 2.2 Specific aims:. 26 3 Materials and methods . 27 3.1 Study participants . 27 3.2 Isolation of peripheral blood mononuclear cells . 27 3.3 Sample freezing and storage . 27 3.4 Phospho protein staining for validation of protocol. 27
Natural tilings and free space in zeolites: models, statistics, correlations, prediction

Abstract We review two concepts in description of free space in the zeolite-like frameworks: topological (natural tiling) and geometrical-topological (Voronoi net). Advantages and disadvantages as well as similarities and differences of both concepts are discussed. We also consider the packing model of zeolite framework assemblage, which is derived from the natural tiling approach. New statistical data are given for natural tilings and Voronoi models of all known 239 zeolite frameworks. A route to modeling and prediction of new zeolite frameworks is outlined.
Electronic Origin of Oxygen Transport Behavior in La-Based Perovskites: A Density Functional Theory Study

Understanding the oxygen transport behavior in perovskites is of central importance for tailoring their physical and chemical properties to various practical applications. In this contribution, periodic DFT+U calculations have been performed to unravel the electronic origin of the oxygen mobility difference in La-based perovskites involving 3d-block transition metals from Sc through Cu. Calculated results indicate that the perovskites generally exhibit an increased reducibility on going from LaScO3 to LaCuO3, and the exceptionally high oxygen vacancy formation energy in LaFeO3 is due to the significant lowering of the electron exchange stabilization upon reduction. The oxygen migration barrier in the first four perovskites varies from 1.2 to 2.1 eV while that for the later five materials is much lower and lies between 0.4 and 0.9 eV. Electronic structure analysis indicates this abrupt change in the migration barrier can be attributed to the different degrees of charge redistribution on the central transit.
Modelagem da produção de energia eólica via equações diferenciais estocásticas

Renewable energies have increased their relevance in the composition of the world’s energy matrix. In particular, in Portugal, wind energy corresponds to 27.5 % of all energy production, being the second largest energy source in the country. The diversification of the energy matrix requires adequate means for forecasting production from different sources, so that the management of energy resources is automatic and efficient. Wind energy presents a special challenge in this context, as it is a highly complex phenomenon with intensely non-linear behavior and with high variability. This work addresses this issue by modeling the energy production of the set of wind turbines placed in continental Portugal using Stochastic Differential Equations (SDEs), based on a set of available observations. For this, we develop the mathematical and statistical tooling for three parametric models of SDEs, including the presentation of the models, development of tools for estimating the model parameters, residual analysis and forecasting. Finally, this framework is applied to the available dataset of real observations conserning this set. We found that SDEs have produced useful results for the management of wind energy production, however there would be an interest in evolving towards SDEs models that are more resilient to large variations in short periods of time, in order to obtain more reliable forecasts. Among these models would be, for example, the models of non-parametric SDEs.
Reducible Inverse CeOx-Based Catalyst as a Potential Candidate for Electroreduction

The inverse metal oxide/metal catalyst is very suitable for electrochemical reaction due to unique catalytic properties of metal oxide with small size and good conductivity of metal. To clarify the potential applications of inverse catalyst in electrochemistry, especially for reducible oxides, an inverse CeOx/Ag(111) model electrocatalyst was constructed and investigated by Density Functional Theory (DFT) for CO2 electrochemical reduction. It is found that Ag atoms acting as an electron donor, can partially reduce Ce4+ to Ce3+ in the supported CeOx cluster leading to the formation of interfacial Ce3+ active sites, which could promote the adsorption and reduction of CO2. As expected, all elementary reaction involved in the CO2 electrochemical reduction are more facile on CeOx/Ag(111) than pure Ag catalyst. Besides, the generation of CH3OH and CH4 is favored on CeOx/Ag(111), whereas the formation of CO, CH2O and H2 is obviously suppressed. More importantly, the weak interaction between H2O and CeOx cluster is beneficial for the desorption of OH intermediate, which makes the regeneration of the catalyst become easier and result in a great recyclability. All those results demonstrate that CeOx/Ag(111) is a potential excellent electrochemical catalyst.
Selective Electrochemical Determination of Etoposide Using a Molecularly Imprinted Overoxidized Polypyrrole Coated Glassy Carbon Electrode

A simple and efficient new electrochemical sensor based on molecularly imprinted polymer has been developed for selective detection of an anticancer agent Etoposide (ETP). The sensor was prepared by electropolymerization via cyclic voltammetry (CV) of pyrrole onto a glassy carbon electrode (GCE) in the presence of ETP molecules. The extraction of ETP molecules embedded in the polymeric matrix was carried out by overoxidation in sodium hydroxide medium using CV. Various important parameters affecting the performance of the imprinted film (MIP) coated sensor were studied and optimized using differential pulse voltammetry (DPV). Under optimal conditions, the sensor response exhibited a linear dependence on ETP concentration (R2= 0.999) over the range 5.0×10−7M – 1.0×10−5M with a LOD (3σ/m) of 2.8×10−9M. The precision (% RSD, n=6) of the proposed sensor for intra- and interdays was found to be 0.84 and 2.46%, respectively. The selectivity of MIP/GCE sensor toward ETP was investigated in the presence of different interfering molecules including excipients and ETP metabolites. The developed sensor showed great recognition ability toward ETP and was successfully applied for its determination in injectable dosage forms and biological human fluids.
Uptake and Leaching of Cu, Cd, and Cr after
EDTA Application in Sand Columns Using
Sorghum and Pearl Millet

In a greenhouse experiment using sand columns, sorghum and pearl millet were grown and spiked with metal solutions of Cu, Cd, and Cr in two concentrations. The chelating agent EDTA was applied to one-month-old plants and metal mobilization was observed through uptake by the plants or leaching through the columns during a period of one month. Growth was much better in pearl millet than sorghum under metal stress. Metal uptake was significantly higher in sorghum and was in the order root>shoot>leaves in both the plants. Metals were differentially mobilized in the order of Cu>Cr>Cd as shown by plant uptake and leaching through the columns. The root to shoot translocation of Cd was significantly improved after EDTA application, and to some extent for Cu but not for Cr. The leaching of metals was the maximum in the second week of application and was almost negligible by the fourth week conforming to the amount of EDTA detected in the leachate. Leaching of Cr differed in the maximum amount at the time of chelant application, while Cu and Cd showed maximum leaching after 7 days. As compared to sorghum, pearl millet was better at controlling leaching because of its extensive root
Catalytic Transfer Hydrogenolysis Reactions for Lignin Valorization to Fuels and Chemicals

Lignocellulosic biomass is an abundant renewable source of chemicals and fuels. Lignin, one of biomass main structural components being widely available as by-product in the pulp and paper industry and in the process of second generation bioethanol, can provide phenolic and aromatic compounds that can be utilized for the manufacture of a wide variety of polymers, fuels, and other high added value products. The effective depolymerisation of lignin into its primary building blocks remains a challenge with regard to conversion degree and monomers selectivity and stability. This review article focuses on the state of the art in the liquid phase reductive depolymerisation of lignin under relatively mild conditions via catalytic hydrogenolysis/hydrogenation reactions, discussing the effect of lignin type/origin, hydrogen donor solvents, and related transfer hydrogenation or reforming pathways, catalysts, and reaction conditions.
Convenient and Efficient Elimination of Heavy Metals from Wastewater Using Smart Pouch with Biomaterial

A newly developed Smart Pouch with enclosed biomaterial (Aloe vera and coconut husk powder) has been experimented for elimination of heavy metals i.e. (Pb2+, Cu2+, Ni2+ and Zn2+) from wastewater. The effect of concentration, pH, temperature, contact duration etc. was investigated using batch experiments which resulted that the Pouch may be accepted for convenient, efficient and low-cost accumulation of several heavy metals simultaneously from waste water. The maximum Pb removal was 99.99%, 93.21% for Cu, and for Ni, it was 91.97% whereas for Zn, 86.41% was obtained and also, the uptake capacity of pouch was quite sensitive towards initial metal concentration in the studied range of 10-200mg/L present in wastewater. The findings were further interpreted by quantum chemical study as theoretical support, various adsorption isotherms, FTIR, SEM, XRD, and physiochemical properties of metal ions to justify the synergized performance of new Pouch. A good correlation was found between experimental methods and theoretical findings.
Resumption of Meiotic Maturation of Oocytes, Pre- and Post-Implantational Embryonic Mortality under Conditions of Experimental Glomerulonephritis and Treatment of Silver Nanoparticles

The aim of the current study was to estimate the resumption of meiotic maturation of oocytes, preand post-implantation mortality of embryos under conditions of experimental glomerulonephritis and intravenous treatment of silver nanoparticles in mice. Experimental glomerulonephritis in mice was achieved by immunization of white laboratory mice of the first generation with a kidney antigen suspension derived from a parent. The treatment was carried out in the following way: Kidney antigen suspension intraperitoneal three times 1 time per day; the procedure was repeated in 3 weeks, one time intraperitoneally with the same dose (10 mkL of suspension per 10 grams of body weight of the animal). Silver nanoparticles (AgNPs, 30 nm) intravenous treatment three times: 1 time per day for 1 h before immunization of animals with suspension of kidney antigen; as well as in 3 weeks once with the same dose (2 mg/kg). Thus, the number of oocytes that resumed meiosis in vitro from animals under experimental glomerulonephritis decreased as compared to the numbers in control animals; no inhibition of meiotic resumption of oocytes of animals was established under conditions of AgNPs treatment; the AgNPs treatment under conditions of experimental glomerulonephritis increased the number of oocytes that resumed meiosis in vitro compared with such values in the control and under conditions of experimental glomerulonephritis. The value of post-implantation embryonic mortality increased under conditions of experimental glomerulonephritis; no infertility of implantation in females of mice under conditions of AgNPs treatment; the AgNPs treatment under conditions of experimental glomerulonephritis decreased post-implantation mortality of embryos.
Mesostructured cellular foam MCF-(9.2T-3D) silica as support for free α-amylase in liquefaction of tapioca starch

As ethanol can be made from insoluble starches, liquefaction of tapioca using α-amylase immobilised on MCF-(9.2T-3D) silica is studied to observe characteristics of the process. The free a-amylase SQzyme BAP was immobilised on the support via adsorption. During immobilisation, temperature and and agitation speed showed low effects on the process, but pH of buffer solution affected the process highly. The optimum enzyme immobilisation occurred at the temperature of 50°C, pH 6 and speed of 60-100 rpm giving the immobilisation efficiency of more than 80%. Liquefaction of the insoluble starch (tapioca) was conducted with the immobilised α-amylase. The maximum result of ± 50% DE was obtained. The experimental factors of buffer pH, temperature and agitation speed changed the DE significantly, but concentration of immobilised enzyme and substrate affected the process lowly. The optimum pH, agitation speed, immobilised enzyme concentration and temperature were 6, 100 rpm, 84.8 U and 80°C, respectively.