Miracle-dz/UniFAR-FTUs huggingface dataset:
Caractérisation du site actif de la relaxase d’ICESt3 de Streptococcus thermophilus

Le transfert horizontal d’elements genetiques joue un role cle dans l’evolution des genomes bacteriens. Parmi ces elements, certains sont capables de se transferer par conjugaison, c’est le cas des elements integratifs conjugatifs (ICE). La relaxase, qui est une proteine essentielle pour ces elements conjugatifs, est une endonuclease simple brin qui initie le transfert de l’element. L’objectif de ce stage est la caracterisation du site actif de la relaxase d’ICESt3, un ICE retrouve chez Streptococcus thermophilus, et membre d’une famille particulierement representee au sein des firmicutes. Cette relaxase presente la particularite d’appartenir a une nouvelle famille de relaxases (famille MOBT) qui n’a a ce jour jamais ete etudiee biochimiquement. Le site actif de cette relaxase a ete mute au niveau de differents residus susceptibles d’etre impliques dans l’activite de la proteine, ou indirectement dans la coordination d’un cofacteur metallique souvent utilise par ce type d’enzyme. Apres avoir standardise un test d’activite de la relaxase, des proteines mutantes ont ete produites et testees. Les resultats ont permis de determiner les acides amines impliques dans l’activite de la relaxase ainsi que ceux permettant la coordination du cation.
Sino-Nasal Changes Associated with Midfacial Expansion: An Overview

The concept of palatal expansion can be viewed as an anachronism since the delivery and scope of this clinical technique has changed dramatically over the past few decades. Indeed, since the palatal complex does not exist in isolation, clinicians ought to be cognizant of how palatal expansion affects contiguous midfacial structures. Because of this structural arrangement, surgical and non-surgical palatal expansion can have clinical consequences on the dentoalveolar structures, which are dependent on bony remodeling of the maxillo-palatine complex. In addition, it can also be suggested that morphologic alterations of the maxillary air sinus might lead to functional and clinical improvements of inflammatory changes associated with rhinosinusitis. Furthermore, enhancements in the nasal airway could affect a host of other conditions, including nasal breathing and obstructive sleep apnea, etc. Therefore, the aim of this chapter is to review the effects of midfacial expansion techniques on contiguous structures, including the paranasal sinuses.
A novel method of low-dimensional representation for temporal behavior of flow fields using deep autoencoder

A method capable of comparing and analyzing the spatio-temporal structures of unsteady flow fields has not yet been established. Temporal analyses of unsteady flow fields are often done after the data of the fields are reduced to low-dimensional quantities such as forces acting on objects. Such an approach is disadvantageous as information about the flow field is lost. There are several data-driven low-dimensional representation methods that preserve the information of spatial structure; however, their use is limited due to their linearity. In this paper, we propose a method for analyzing the time series data of unsteady flow fields. We firstly propose a data-driven nonlinear low-dimensional representation method for unsteady flow fields that preserves its spatial structure; this method uses a convolutional autoencoder, which is a deep learning technique. In our proposed method, the spatio-temporal structure can be represented as a trajectory in a low-dimensional space using the visualization technique originally proposed for dynamic networks. We applied the proposed method to unsteady flows around a two-dimensional airfoil and demonstrated that it could briefly represents the changes in the spatial structure of the unsteady flow field over time. This method was demonstrated to also be able to visualize changes in the quasi-periodic state of the flow when the angle of attack of the airfoil was changed. Furthermore, we demonstrated that this method is able to compare flow fields that are constructed using different conditions such as different Reynolds numbers and angles of attack.
Lab-Scale Biodegradation Study of BTEX under the Unsaturated Condition and Its Effect on Soil Matric Potential

ABSTRACT Benzene, toluene, ethylbenzene, and xylene are collectively known as BTEX which contributes to volatile environmental contaminants. This present study investigates the microbial degradation of BTEX in batch and continuous soil column experiments and its effects on soil matric potential. Batch degradation experiments were performed with different initial concentrations of BTEX using the BTEX tolerant culture isolated from petroleum-contaminated soil. In batch study, the degradation pattern for single substrate showed that xylene was degraded much faster than other compounds followed by ethylbenzene, toluene, and benzene with the highest μmax = 0.140 h−1 during initial substrate concentration of 100 mg L−1. Continuous degradation experiments were performed in a soil column with an inlet concentration of BTEX of about 2000 mg L−1 under unsaturated flow in anaerobic condition. BTEX degradation pattern was studied with time and the matric potential of the soil at different parts along the length of the column were determined at the end of the experiment. In continuous degradation study, BTEX compounds were degraded with different degradation pattern and an increase in soil matric potential was observed with an increase in depth from top to bottom in the column with applied suction head. It was found that column biodegradation contributed to 69.5% of BTEX reduction and the bacterial growth increased the soil matric potential of about 34% on an average along the column height. Therefore, this study proves that it is significant to consider soil matric potential in modeling fate and transport of BTEX in unsaturated soils.
Most favorable stimulation duration in the sensorimotor cortex for fNIRS-based BCI.

One of the primary objectives of the brain-computer interface (BCI) is to obtain a command with higher classification accuracy within the shortest possible time duration. Therefore, this study evaluates several stimulation durations to propose a duration that can yield the highest classification accuracy. Furthermore, this study aims to address the inherent delay in the hemodynamic responses (HRs) for the command generation time. To this end, HRs in the sensorimotor cortex were evaluated for the functional near-infrared spectroscopy (fNIRS)-based BCI. To evoke brain activity, right-hand-index finger poking and tapping tasks were used. In this study, six different stimulation durations (i.e., 1, 3, 5, 7, 10, and 15 s) were tested on 10 healthy male subjects. Upon stimulation, different temporal features and multiple time windows were utilized to extract temporal features. The extracted features were then classified using linear discriminant analysis. The classification results using the main HR showed that a 5 s stimulation duration could yield the highest classification accuracy, i.e., 74%, with a combination of the mean and maximum value features. However, the results were not significantly different from the classification accuracy obtained using the 15 s stimulation. To further validate the results, a classification using the initial dip was performed. The results obtained endorsed the finding with an average classification accuracy of 73.5% using the features of minimum peak and skewness in the 5 s window. The results based on classification using the initial dip for 5 s were significantly different from all other tested stimulation durations (p < 0.05) for all feature combinations. Moreover, from the visual inspection of the HRs, it is observed that the initial dip occurred as soon as the task started, but the main HR had a delay of more than 2 s. Another interesting finding is that impulsive stimulation in the sensorimotor cortex can result in the generation of a clearer initial dip phenomenon. The results reveal that the command for the fNIRS-based BCI can be generated using the 5 s stimulation duration. In conclusion, the use of the initial dip can reduce the time taken for the generation of commands and can be used to achieve a higher classification accuracy for the fNIRS-BCI within a 5 s task duration rather than relying on longer durations.
Inhibition of gram negative bacterial growth and biofilm formation by alpha thujone

The increasing resistance of microorganism to antibiotics in the last decades, drove microbiologists, botanists, and natural-products chemists to search for phytochemicals that could be used for treatment of infectious diseases. Essential oils, which are derived from plants, such as thujone, have been recognized to display many biological activities many of which needed more exploration. This study was designed to test the ability of alpha thujone to inhibit the growth and biofilm formation of clinical bacterial isolates. The agar dilution method used to detect the antibacterial effect of alpha thujone, revealed that at high concentrations (30 mg/ml and 15 mg/ml) alpha thujone showed some antibacterial activity on some of the Gram-negative isolates tested. It was evident, however, and after using standard tests for detection of the inhibition of biofilm formation, that alpha thujone, at low concentrations (3.8 mg/ml) demonstrated an inhibitory effect on the biofilm formation of most of the different bacterial strains tested. This previously uncovered characteristic of alpha thujone, may prove to be very useful in preventing infections by primary pathogens.
Plant biomass degradation supported by non-enzymatic proteins

Lignocellulosic biomass, rich in potential carbon sources and value added products, has been intensively investigated in scope of its costefficient and effective decomposition. Many methods were developed, physicochemical or biological. Nevertheless, they are either expensive, inefficient or pose threat to the environment. Recently discovered proteins, lacking any hydrolytic activity, can be a key to solve problems associated with a slow process of enzymatical, eco-friendly degradation. These proteins belong to three related groups – swollenins, expansins and loosenins. Using different molecular mechanisms, they disrupt hydrogen bonds within cellulose chains, enabling enzymes to perform hydrolysis leading to decomposition of lignocellulosic complex.
Synthesis, Single Crystal X-ray Structure, DFT Computations, Hirshfeld Surface Analysis and Molecular Docking Simulations on ({[(1E)-1-(1,3-Benzodioxol-5-yl)-3-(1H-imidazol-1-yl)propylidene]amino}oxy)(furan-2-yl)methanone: A New Antifungal Agent

The development of drug-resistance and high morbidity rates due to life-threatening fungal infections account for a major global health problem. A new antifungal imidazole-based oximino ester 5 has been prepared and characterized with the aid of different spectroscopic tools. Single crystal X-ray analysis doubtlessly identified the (E)-configuration of the imine fragment of the title compound. Compound 5, C18H15N3O5, was crystallized in the monoclinic, P21/c, a = 10.4067 (5) Å, b = 6.8534 (3) Å, c = 23.2437 (12) Å, β = 94.627 (2)°, V = 1652.37 (14) Å3, Z = 4. Spectral and electronic features of compound 5 have been thoroughly explored with the aid of density function theory (DFT) simulations and the data were compared with the experimental results. In addition, Hirshfeld surface analysis and molecular docking simulations were executed on the target compound. Molecular docking results are fairly consistent with the experimental in vitro antifungal potential of the oximino ester 5.
Lignin Degrading System of Phanerochaete
chrysosporium and its Exploitation
for Degradation of Synthetic Dyes Wastewater

Azo dyes are the main group of dyes used in different industrial applications. These dyes are highly toxic for aquatic life, so their removal is of utmost importance before they can be disposed of in a main water body. The present study focused on degrading/mineralizing the synthetic reactive dye wastewater. Initial experiments were done with four indigenous white rot fungi. P. chrysosporium (PC) showed more potential toward degradation of synthetic dye wastewater than other three fungal strains, so it was selected for further optimization of different fermentation parameters. Maximum decolorization (84.8%) of reactive dye wastewater was obtained at pH 5, inoculum size 4 mL, and 30oC. After optimizing experimental parameters, the effects of different nutritional factors like carbon and nitrogen sources were also studied. Decolorization of synthetic dye wastewater was increased from 84.8 to 89.2%, when rice bran was used as an additional carbon source. However, no increase in decolorization of synthetic dye wastewater was observed in the presence of nitrogen supplements. The screened fungal strain decolorized the wastewater up to 90%. The effect of different nutritional factors enhanced the degradation capability of the fungal strain under study. UV-visible and FTIR analyses confirmed the degradation of synthetic dye wastewater into simpler, non-toxic products.
Enhancement of lytic polysaccharide monooxygenase activity derived from Neurospora sp. in solid substrate fermentation of oil palm empty fruit bunch

Oil Palm Empty Fruit Bunches (OPEFB) are lignocellulose by products which are generated from oil palm fruit pressing. To date, OPEFB were mainly burnt to generate energy and often contribute to air pollutions. Therefore, OPEFB utilization into more valuable products is timely demanded. Component of OPEFB is classified as lignocelluloses family where cellulose is the major component (46%), followed by hemicellulose (34%) and lignin (20%), these complex components must be degraded into smaller molecules before further downstream bioconversion. In this study, OPEFB degradation was conducted biologically employing Neurospora sp. due to its ability in producing cellulases and Lytic Polysaccharide Monooxygenase (LPMO). The objectives of this study were to examine OPEFB degradation employing Neurospora in solid substrate fermentation and detection of LPMO activity derived from Neurospora. Neurospora intermedia isolate O3 could produce 11.9 ± 0.4 µmol/g reducing sugars when incubated for three days in OPEFB without delignification, while it increased to 77.4±2.3 µmol/g in OPEFB with delignification treatment. Interestingly, copper ion supplementation into OPEFB medium significantly increased in reducing sugar production up to 172.9±15.0 µmol/g, which might be due to the enhancement of LPMO activity.
Effect of divergence angle of ejector nozzle on aerosolisation of powdered nanoparticles

ABSTRACT A combined experimental-numerical study was performed to reveal the mechanisms of powdered SiO2 nanoparticle (NP) breakage and establish the relationship between the divergent angle (α) of a convergent-divergent (C-D) nozzle and nanoparticle size distribution. All distributions of aerosolised SiO2 NPs obtained through ejectors with varied α were identically log-normal and unimodal. As α increased (from 8° to 20°), there were identified decreases in Geometric Mean Distribution (GMD)(from 216 to 189 nm), mode diameter, and median diameter, while Geometric Standard Deviation (GSD) increased slightly (from 1.59 to 1.65). The parallel negative growth trends of D25 and D75, with slightly decreasing interquartile (D25–D75) ranges, indicated that an increase in α could result in a clear shift of Particle Sizes Distribution(PSD) towards smaller particle sizes. This implied that NP deagglomeration was strengthened and the ejector became more efficient as α increased. Three cross-sections including the C-D nozzle outlet (Section 1), mixer tube inlet (Section 2), and central section (Section 3) were selected to estimate the influence of shear stress (|τ|) distribution in the ejector on NP aerosolisation. Increasing α hardly changed the location of the two inner peaks, but it significantly decreased the values of inner peaks and smoothened |τ| distributions. |τ| in Section 2 with different α exhibited a flat bimodal distribution and the two outer steep peaks (from Section 1) disappeared. For |τ0| = 0.5 and |τ0| = 1 Pa, the ratio of the |τ| distribution range of |τ| > |τ0| (0.5 Pa < |τ0|< 5 Pa) to the entire section span, η, increased significantly as α increased. The growth rate of η decreased apparently for |τ0| ranging from 2 to 4 Pa, but for |τ0| ≥ 5 Pa, η stopped growing in Section 1. The maximum value of |τ| exerted no significant influence on NP dispersion. The smoothness and flatness of the |τ| distribution determined whether the powdered NPs could experience enough shear aerodynamics and be dispersed thoroughly. This played a crucial role in NP aerosolisation. The mechanism of the effect of α on NP dispersion resulted in smooth and flat |τ| distributions. This helped expand |τ| distribution to increase the possibility of powdered NPs experiencing stronger shear flow as α increased.
CO2 Adsorption on Premodified Li/Al Hydrotalcite Impregnated with Polyethylenimine

In this study, Li/Al hydrotalcite (HT) was treated with calcination and potassium hydroxyl-ethanol to form bcHT (basic-modified calcined hydrotalcite). This material was then polyethylenimine (PEI)-functionalized to create a new sorbent that has ultralow energy consumption. Various methods were applied to characterize the sorbent, including N2 adsorption–desorption, Fourier transform infrared spectroscopy, X-ray diffraction, and scanning electron microscopy. CO2 adsorption capacity, which was affected by PEI loadings and adsorption temperatures, was assessed with the CO2 adsorption isotherms and cyclic CO2 adsorption–desorption performance. Results showed that the optimal CO2 adsorption capacity of 1.723 mmol/g was reached when operating with temperature of 323 K and PEI loading of 40%. The Freundlich model was applied to provide optimal correlations with the experimental data, and the correlation coefficients reached 0.997. The average isosteric heat of CO2 adsorption was calculated to be 67.492 kJ/mol.
COMPARATIVE EFFECT BETWEEN CHITOSAN AND CHITOSAN- Cu COMPLEX ON CARBON-TETRACHLORIDE (CCL4) INDUCED LIVER DAMAGE IN RATS

BACKGROUND: Carbon tetrachloride (CCl4 ) is a toxic material known to induce lipid peroxidation and liver damage. The possible protective roles that involved by chitosan or chitosan-Cu complex against CCl4 induced liver intoxication were investigated in male rats. RESULTS: CCl4 administred at dose 20 mg/kg body weight i.p., exceed malondialdehyde (MDA) and protein carbonyle (PC), depleted superoxide dismutase (SOD) and glutathione (GSH), in concomitant with marked increase in investigated liver function parameters , alanine aminotransferase and aspartate aminotransferase (ALT, AST), impaired serum and liver total protein , albumin and globulin. An elevation in serum and hepatic total lipids, total cholesterol, triglycerides and serum LDL and VLDL levels as well as a low level of HDL were recorded. In the same time, there was a significant increase in sodium and iron contents in the serum while a significant decrease in potassium and zinc contents were recorded. Animals pretreated with chitosan (200 mg /kg body weight) orally by stomach tube for 21 consecutive days prior to CCl4 challenge significantly attenuated most of the tested parameters, strengthen antioxidant defense system, ameliorated liver function effectively. Chitosan-Cu complex has a protective effect by a higher degree than that of chitosan only. CONCLUSION: These findings suggest that pretreatment with chitosan-Cu complex has higher hepato-protective effects than that of only chitosan against CCl4 induced toxicity in rat.
Adsorption of Chromium in Aqueous Solution by Using Zeolite A Prepared from Fly Ash

Adsorption of Cr(III) and Cr(VI) in aqueous solution by the zeolite A from coal fly ash at various conditions has been carried out. Zeolite A was synthesized from fly ash through modified alkaline fusion hydrothermal process in a reactor stainless steel. Adsorption is carried out by direct contact between the adsorbent and adsorbate in an adsorption batch. Zeolite A from fly ash (ZA-FA) of 0.01 g was mixed with 20 mL both Cr(III) and Cr(VI) at various pH, contact time and initial concentration, in a flask Erlenmeyer 50 mL. The result showed that pH conditions of adsorption process, affect the adsorption ability of zeolite A to Cr(III) and Cr(VI) in aqueous solution. The adsorption of Cr(III) and Cr(VI) on zeolite A reached a maximum at pH 6 and time contact 120 minutes. The adsorption of Cr(III) on zeolite A increased from 3.4 mg/g at pH 3 and achieved a maximum adsorption of 42.67 mg/g at pH 6. At higher pH (7-8) the Cr(III) adsorption tends decreases. The adsorption ability of ZA-FA to Cr(III) is higher than that of Cr(VI) in aqueous solution. The Cr(III) adsorption process on ZA-FA follows the pseudo-order 2 kinetics model.
The Removal of Heavy Metals from the Leachate of Aged Landfill: The Application of the Fenton Process and Nanosilica Absorbent

Since leachate is typically composed of numerous constituents, its management requires special attention. After the raw leachate of Saravan in Rasht (Guilan Province, Iran) was transferred to a laboratory and its specifications were determined, it was subjected to experiments by the bench-scale method. The analyses of pH and heavy metals were performed in the main and control anaerobic reactors at time zero, before precipitation, and two hours after precipitation. After the anaerobic process was over and the optimal retention time was identified in the anaerobic reactor, the removal of heavy metals was analyzed by the Fenton process and nanosilica absorbent in leachate treatment. In the primary anaerobic reactor, the highest and lowest removal rates were 59 and 39% for Ni and Cu, respectively. In the Fenton process with optimal H2O2/Fe+2 ratio, Cu and Hg showed the lowest and highest removal rates of 22.4 and 54.54%, respectively. At the optimal rate of nanosilica absorbent and the retention time of 15 min, As was removed maximally with an efficiency of 38% and Cu was removed minimally. The results revealed that the integration of the anaerobic process with the Fenton process and nanosilica absorbent was very effective in removing heavy metals from the aged landfill leachate.
Interseismic Deformation From Sentinel‐1 Burst‐Overlap Interferometry: Application to the Southern Dead Sea Fault

Interferometric Synthetic Aperture Radar (InSAR) data are increasingly being used to map interseismic deformation with ascending and descending‐orbit observations allowing for resolving the near‐east and vertical displacement components. The north component has, however, been difficult to retrieve due to the limited sensitivity of standard InSAR observations in that direction. Here, we address this problem by using time‐series analysis of along‐track interferometric observations in burst‐overlap areas of the Terrain Observation with Progressive Scan imaging mode of the Sentinel‐1 radar satellites. We apply this method to the southern part of the near‐north striking Dead Sea transform fault to show that the ∼5 mm/year relative motion is well recovered. Furthermore, the results indicate the locking depth of the fault decreases toward the south as it enters the transtensional Gulf of Aqaba basin. Our results show that time‐series analysis of burst‐overlap interferometric observations can be used to obtain meaningful interseismic deformation rates of slow‐moving and northerly striking faults.