Miracle-dz/UniFAR-FTUs huggingface dataset:
Mouthwash Containing Vitamin E, Triamcinolon, and Hyaluronic Acid Compared to Triamcinolone Mouthwash Alone in Patients With Radiotherapy-Induced Oral Mucositis: Randomized Clinical Trial

One of the most common side effects of radiotherapy in head and neck cancers is mucositis. Despite all the studies conducted on new therapies proposed for oral mucositis caused by radiation therapy, a single standard treatment strategy has not been developed yet. In the present study, for the first time, the effectiveness of the treatment with a combined mouthwash containing vitamin E (as an antioxidant), triamcinolone (as an anti-inflammatory agent) and hyaluronic acid (HA) (as a local reducer used for reducing the effects of ROS on the mucosa, with ameliorative effects (improving the healing process) compared to triamcinolone mouthwash alone was investigated in patients with radiotherapy-induced oral mucositis. This study was a randomized triple-blind clinical trial performed on 60 patients underwent radiotherapy on an outpatient basis. The combined mouthwash containing vitamin E, triamcinolone, and hyaluronic acid compared to triamcinolone mouthwash alone was prescribed for 4 weeks. The severity of oral mucositis was assessed based on the WHO classification and the intensity of pain was assessed using the numerical pain intensity scale. According to the analysis performed in the first, second, third and fourth weeks, the reduction of oral mucositis grade in the intervention group was significantly higher than in the comparison group. In the first, second, third, and fourth weeks, the reduction in pain intensity in the intervention group was significantly higher than in the comparison group (P < 0.001). The combined mouthwash containing vitamin E, hyaluronic acid and triamcinolone acetonide can be used as an effective treatment for oral mucositis caused by radiation therapy, which is probably the result of antioxidant, anti-inflammatory and improved healing process mechanisms due to the biological nature of the components of this mouthwash. Trial registration This study was registered in the WHO Primary registry (IRCT) with the code IRCT20190428043407N. Registered on 20 July 2019, https://www.irct. ir/trial/39231.
Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in Pisum sativum

Transition to flowering is an important stage of plant development. Many regulatory modules that control floral transition are conservative across plants. This process is best studied for the model plant Arabidopsis thaliana. The homologues of Arabidopsis genes responsible for the flowering initiation in legumes have been identified, and available data on their expression provide a good basis for gene network modeling. In this study, we developed several dynamical models of a gene network controlling transition to flowering in pea (Pisum sativum) using two different approaches. We used differential equations for modeling a previously proposed gene regulation scheme of floral initiation in pea and tested possible alternative hypothesis about some regulations. As the second approach, we applied neural networks to infer interactions between genes in the network directly from gene expression data. All models were verified on previously published experimental data on the dynamic expression of the main genes in the wild type and in three mutant genotypes. Based on modeling results, we made conclusions about the functionality of the previously proposed interactions in the gene network and about the influence of different growing conditions on the network architecture. It was shown that regulation of the PIM, FTa1, and FTc genes in pea does not correspond to the previously proposed hypotheses. The modeling suggests that short- and long-day growing conditions are characterized by different gene network architectures. Overall, the results obtained can be used to plan new experiments and create more accurate models to study the flowering initiation in pea and, in a broader context, in legumes.
Stress–Strain Index Map: A New Way to Represent Corneal Material Stiffness

Purpose To introduce a new method to map the mechanical stiffness of healthy and keratoconic corneas. Methods Numerical modeling based on the finite element method was used to carry out inverse analysis of simulated healthy and keratoconic corneas to determine the regional variation of mechanical stiffness across the corneal surface based on established trends in collagen fibril distribution. The Stress–Strain Index (SSI), developed and validated in an earlier study and presented as a parameter that can estimate the overall stress–strain behavior of corneal tissue, was adopted in this research as a measure of corneal stiffness. The regional variation of SSI across the corneal surface was estimated using inverse analysis while referring to the common features of collagen fibrils’ distribution obtained from earlier x-ray scattering studies. Additionally, for keratoconic corneas, a method relating keratoconic cone features and cornea’s refractive power to the reduction in collagen fibril density inside the cone was implemented in the development of SSI maps. In addition to the simulated cases, the study also included two keratoconus cases, for which SSI maps were developed. Results SSI values varied slightly across corneal surface in the simulated healthy eyes. In contrast, both simulated and clinical keratoconic corneas demonstrated substantial reductions in SSI values inside the cone. These SSI reductions depended on the extent of the disease and increased with more considerable simulated losses in fibril density in the cone area. SSI values and their regional variation showed little change with changes in IOP, corneal thickness, and curvature. Conclusion SSI maps provide an estimation of the regional variation of biomechanical stiffness across the corneal surface. The maps could be particularly useful in keratoconic corneas, demonstrating the dependence of corneal biomechanical behavior on the tissue’s microstructure and offering a tool to fundamentally understand the mechanics of keratoconus progression in individual patients.
Nucleophosmin Protein Dephosphorylation by DUSP3 Is a Fine-Tuning Regulator of p53 Signaling to Maintain Genomic Stability

The dual-specificity phosphatase 3 (DUSP3), an atypical protein tyrosine phosphatase (PTP), regulates cell cycle checkpoints and DNA repair pathways under conditions of genotoxic stress. DUSP3 interacts with the nucleophosmin protein (NPM) in the cell nucleus after UV-radiation, implying a potential role for this interaction in mechanisms of genomic stability. Here, we show a high-affinity binding between DUSP3-NPM and NPM tyrosine phosphorylation after UV stress, which is increased in DUSP3 knockdown cells. Specific antibodies designed to the four phosphorylated NPM’s tyrosines revealed that DUSP3 dephosphorylates Y29, Y67, and Y271 after UV-radiation. DUSP3 knockdown causes early nucleolus exit of NPM and ARF proteins allowing them to disrupt the HDM2-p53 interaction in the nucleoplasm after UV-stress. The anticipated p53 release from proteasome degradation increased p53-Ser15 phosphorylation, prolonged p53 half-life, and enhanced p53 transcriptional activity. The regular dephosphorylation of NPM’s tyrosines by DUSP3 balances the p53 functioning and favors the repair of UV-promoted DNA lesions needed for the maintenance of genomic stability.
Stability Studies on Immobilized Glucose Oxidase Usingan Amperometric Biosensor – Effect of Protein Based Stabilizing Agents

A simple amperometric biosensor was used to study the stability of glucose oxidase (GOD) immobilized with different protein based stabilizing agents (PBSA) against temperature, pH and urea concentrations. Lysozyme as PBSA showed signi®cant increase in the stability of soluble as well as immobilized GOD compared to BSA and gelatin. At pH 6.0, the transition temperature (Tm) of the GOD immobilized with lysozyme was found to be 74.9 �C whereas that of GOD immobilized with gelatin and BSA were 66.1 �C and 63.8 �C, respectively. GOD immobilized with lysozyme retained more than 50% activity in 8M urea solution whereas with BSA and gelatin most of the activity was lost. More than 3-fold increase in the stability of soluble GOD was observed in presence of lysozyme in 50mM phosphate buffer, pH 6.0 and at 60 �C. A strong adverse in¯uence on stabilization of soluble GOD in presence of 0.2M NaCl indicates that ionic interaction between GOD and lysozyme may be playing a crucial role in the stabilization.
αB-Crystallin Alleviates Endotoxin-Induced Retinal Inflammation and Inhibits Microglial Activation and Autophagy

αB-Crystallin, a member of the small heat shock protein (sHSP) family, plays an immunomodulatory and neuroprotective role by inhibiting microglial activation in several diseases. However, its effect on endotoxin-induced uveitis (EIU) is unclear. Autophagy may be associated with microglial activation, and αB-crystallin is involved in the regulation of autophagy in some cells. The role of αB-crystallin in microglial autophagy is unknown. This study aimed to explore the role of αB-crystallin on retinal microglial autophagy, microglial activation, and neuroinflammation in both cultured BV2 cells and the EIU mouse model. Our results show that αB-crystallin reduced the release of typical proinflammatory cytokines at both the mRNA and protein level, inhibited microglial activation in morphology, and suppressed the expression of autophagy-related molecules and the number of autophagolysosomes in vitro. In the EIU mouse model, αB-crystallin treatment alleviated the release of ocular inflammatory cytokines and the representative signs of inflammation, reduced the apoptosis of ganglion cells, and rescued retinal inflammatory structural and functional damage, as evaluated by optical coherence tomographic and electroretinography. Taken together, these results indicate that αB-crystallin inhibits the activation of microglia and supresses microglial autophagy, ultimately reducing endotoxin-induced neuroinflammation. In conclusion, αB-crystallin provides a novel and promising option for affecting microglial autophagy and alleviating symptoms of ocular inflammatory diseases.
CUTie2: The Attack of the Cyclic Nucleotide Sensor Clones

The detection of small molecules in living cells using genetically encoded FRET sensors has revolutionized our understanding of signaling pathways at the sub-cellular level. However, engineering fluorescent proteins and specific binding domains to create new sensors remains challenging because of the difficulties associated with the large size of the polypeptides involved, and their intrinsically huge conformational variability. Indeed, FRET sensors’ design still relies on vague structural notions, and trial and error combinations of linkers and protein modules. We recently designed a FRET sensor for the second messenger cAMP named CUTie (Cyclic nucleotide Universal Tag for imaging experiments), which granted sub-micrometer resolution in living cells. Here we apply a combination of sequence/structure analysis to produce a new-generation FRET sensor for the second messenger cGMP based on Protein kinase G I (PKGI), which we named CUTie2. Coarse-grained molecular dynamics simulations achieved an exhaustive sampling of the relevant spatio-temporal coordinates providing a quasi-quantitative prediction of the FRET efficiency, as confirmed by in vitro experiments. Moreover, biochemical characterization showed that the cGMP binding module maintains virtually the same affinity and selectivity for its ligand thant the full-length protein. The computational approach proposed here is easily generalizable to other allosteric protein modules, providing a cost effective-strategy for the custom design of FRET sensors.
Recent Advances in Producing Sugar Alcohols and Functional Sugars by Engineering Yarrowia lipolytica

The sugar alcohols and functional sugars have wide applications in food, pharmaceutical, and chemical industries. However, the smaller quantities of natural occurring sugar alcohols and functional sugars restricted their applications. The enzymatic and whole-cell catalyst production is emerging as the predominant alternatives. The properties of Yarrowia lipolytica make it a promising sugar alcohol and functional sugar producer. However, there are still some issues to be resolved. As there exist reviews about the chemical structures, physicochemical properties, biological functions, applications, and biosynthesis of sugar alcohols and/or functional sugars in Y. lipolytica, this mini review will not only update the recent advances in enzymatic and microbial production of sugar alcohols (erythritol, D-threitol, and xylitol) and functional sugars (isomaltulose, trehalose, fructo-oligosaccharides, and galacto-oligosaccharides) by using recombinant Y. lipolytica but also focus on the studies of gene discovery, pathway engineering, expanding substrate scope, bioprocess engineering, and novel breeding methods to resolve the aforementioned issues.
Physicochemical Changes in Hazelnut, Olive Pomace, Grapeseed and Sunflower Oils Heated at Frying Temperatures

In order to compare the thermal performances to evaluate suitability for frying, hazelnut oil (HNO), olive pomace oil (OPO), grapeseed oil (GSO) and sunflower oil (SSO) were heated for 5 h / 5 consecutive days at 175 ± 5 °C, and sampled at the end of each day. Free acidity, peroxide value, conjugated dienes, total polar materials, viscosity, and CIE color values were measured. Highest values of free acidity, conjugated dienes, total polar materials and viscosity were observed in grapeseed oil sample. GSO has reached to a very viscous state during the earlier hours of the operation; hence it is not suitable for frying. Better thermal performances have found with HNO and OPO when compared to the control oil, SSO. Therefore, both oils can alternatively be used as new frying oils effectively.
Spectral Sparsification of Metrics and Kernels

A set of 𝑛 points in a geometric space implicitly induces a complete graph where the weight of an edge between two points is a function of the distance between the endpoints. There are many natural problems that arise from such a geometric graph and many standard geometric problems can be recast as simple properties of this graph. A basic algorithmic obstacle that arises is that the explicit size of the graph is quadratic in the size of the input. There is a long line of research overcoming this obstacle in low-dimensional spaces, as well as some positive results in high-dimensional and more abstract models for speciﬁc applications. Here we consider graph problems in general and address the issue of constructing the geometric graph. Rather than constructing these graphs exactly, we ask if it is possible to explicitly construct a sparse approximation of these geometric graphs in nearly linear time. We consider geometric graphs where the edge weights are given as either as a metric (via an oracle), or given by a smooth kernel function in a Euclidean space. For both of these settings, we show that for any 𝜖 > 0, one can compute an explicit ( 1 + 𝜖 ) -approximate spectral approximation of the geometric graph with ˜ 𝑂 (cid:0) 𝑛 / 𝜖 2 (cid:1) edges in ˜ 𝑂 (cid:0) 𝑛 / 𝜖 2 (cid:1) randomized time. Some of these algorithms are extremely simple. Composed with nearly linear time graph algorithms, this allows for a broad class of applications on geometric graphs with running times proportional to the number of points.
Arabic dialect sentiment analysis with ZERO effort. \\ Case study: Algerian dialect

This paper presents an analytic study showing that it is entirely possible to analyze the Arabic dialect’s sentiment without constructing any resources. The idea of this work is to use the resources dedicated to a given dialect X for analyzing the sentiment of another dialect Y. The unique condition is to have X and Y in the same category of dialects. We apply this idea to the Algerian dialect, a Maghrebi Arabic dialect that suffers from limited available tools and other handling resources required for automatic sentiment analysis. To do this analysis, we rely on Maghrebi dialect resources and two manually annotated sentiment corpus for Tunisian and Moroccan dialect, respectively. We also use a large corpus for the Maghrebi dialect. We use a state-of-the-art system and propose a new deep learning architecture to classify the sentiment of the Algerian dialect automatically. Experimental results show that F1-score is up to 83%. It is achieved by Multilayer Perceptron (MLP) with Tunisian corpus and Long short-term memory (LSTM) with the combination of Tunisian and Moroccan. An improvement of 15% compared to its closest competitor was observed through this study. Ongoing work is aimed at manually constructing an annotated sentiment corpus for the Algerian dialect.
Improving the diagnosis of heart failure in patients with atrial fibrillation

Objective To improve the echocardiographic assessment of heart failure in patients with atrial fibrillation (AF) by comparing conventional averaging of consecutive beats with an index-beat approach, whereby measurements are taken after two cycles with similar R-R interval. Methods Transthoracic echocardiography was performed using a standardised and blinded protocol in patients enrolled in the RATE-AF (RAte control Therapy Evaluation in permanent Atrial Fibrillation) randomised trial. We compared reproducibility of the index-beat and conventional consecutive-beat methods to calculate left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and E/e’ (mitral E wave max/average diastolic tissue Doppler velocity), and assessed intraoperator/interoperator variability, time efficiency and validity against natriuretic peptides. Results 160 patients were included, 46% of whom were women, with a median age of 75 years (IQR 69–82) and a median heart rate of 100 beats per minute (IQR 86–112). The index-beat had the lowest within-beat coefficient of variation for LVEF (32%, vs 51% for 5 consecutive beats and 53% for 10 consecutive beats), GLS (26%, vs 43% and 42%) and E/e’ (25%, vs 41% and 41%). Intraoperator (n=50) and interoperator (n=18) reproducibility were both superior for index-beats and this method was quicker to perform (p<0.001): 35.4 s to measure E/e’ (95% CI 33.1 to 37.8) compared with 44.7 s for 5-beat (95% CI 41.8 to 47.5) and 98.1 s for 10-beat (95% CI 91.7 to 104.4) analyses. Using a single index-beat did not compromise the association of LVEF, GLS or E/e’ with natriuretic peptide levels. Conclusions Compared with averaging of multiple beats in patients with AF, the index-beat approach improves reproducibility and saves time without a negative impact on validity, potentially improving the diagnosis and classification of heart failure in patients with AF.
Geometric Cover with Outliers Removal

We study the problem of partial geometric cover, which asks to find the minimum number of geometric objects (unit squares and unit disks in this work) that cover at least ( n − t ) of n given planar points, where 0 ≤ t ≤ n/ 2. When t = 0, the problem is the classical geometric cover problem, for which many existing works adopt a general framework called the shifting strategy. The shifting strategy is a divide and conquer paradigm which partitions the plane into equal-width strips, applies a local algorithm on each strip and then merges the local solutions with only a small loss on the overall approximation ratio. A challenge to extend the shifting strategy to the case of outliers is to determine the number of outliers in each strip. We develop a shifting strategy incorporating the outlier distribution, which runs in O ( tn log n ) time. We also develop local algorithms on strips for the outliers case, improving the running time over previous algorithms, and consequently obtain approximation algorithms to the partial geometric cover.
High‐quality surface passivation of silicon solar cells in an industrial‐type inline plasma silicon nitride deposition system

We have studied the surface passivation of silicon by deposition of silicon nitride (SiN) in an industrial‐type inline plasma‐enhanced chemical vapor deposition (PECVD) reactor designed for the continuous coating of silicon solar cells with high throughput. An optimization study for the passivation of low‐resistivity p‐type silicon has been performed exploring the dependence of the film quality on key deposition parameters of the system. With the optimized films, excellent passivation properties have been obtained, both on undiffused p‐type silicon and on phosphorus‐diffused n+ emitters. Using a simple design, solar cells with conversion efficiencies above 20% have been fabricated to prove the efficacy of the inline PECVD SiN. The passivation properties of the films are on a par with those of high‐quality films prepared in small‐area laboratory PECVD reactors. Copyright © 2004 John Wiley & Sons, Ltd.
Monodisperse PDLC composites generated by use of polyvinyl alcohol boric acid as matrix

A polymer dispersed liquid crystal composite (PDLC) based on polyvinyl alcohol boric acid (PVAB) as polymer matrix and 4-cyano-4′-penthylbiphenyl (5CB) as liquid crystal has been prepared by an encapsulation method. PVAB was used as a polymer matrix for the first time. Polarized light microscopy, scanning electron microscopy, differential scanning calorimetry and contact angle measurements were employed to explore the obtained PDLC systems. Optical properties were studied by photoluminescence spectroscopy. It was concluded that PVAB promotes homeotropic alignment, uniform distribution and narrow size polydispersity of the liquid crystal droplets. Moreover, the PDLC films show features of biocompatible materials, keeping the promise of their bioapplications.
Double-sided reel-to-reel metal-organic chemical vapor deposition system of YBa2Cu3O7-δ thin films

Two-micrometer thick YBa2Cu3O7-δ (YBCO) films have been successfully deposited on both sides of LaAlO3 single crystalline substrates by using a home-made reel-to-reel metal-organic chemical vapor deposition (MOCVD) system, which has two opposite symmetrical shower heads and a special-designed heater. This technique can simultaneously fabricate double-sided films with high deposition rate up to 500 nm/min, and lead to doubling current carrying capability of YBCO, especially for coated conductors (CCs). X-ray diffraction analysis showed that YBCO films were well crystallized and highly epitaxial with the full width at half maximum values of 0.2° ∼ 0.3° for the rocking curves of (005) YBCO and 1.0° for Φ-scans of (103) YBCO. Scanning electron microscope revealed dense, crack-free, slightly rough surface with Ba-Cu-O precipitates. The films showed critical current density (Jc, 77 K, 0 T) of about 1 MA/cm2, and overall critical current of 400 A/cm, ascribed to the double-sided structure. Our results also demon.
Recombination mechanism and carrier lifetimes of semi‐insulating GaAs:Cr

The recombination process has been investigated in semi‐insulating GaAs Cr. The theoretical model was based on the Shockley–Read statistics considering two traps, the HL1 (Cr) and EL2, respectively. The trap concentrations and the carrier lifetimes have been determined from the dependence of both the photomagnetoelectric effect short‐circuit current and the photoconductance on the illumination intensity.