Search results for: inorganic molecular crystals

Authors: Geno Paul S. Cumla, Jan Mariel M. Gentiles, M. Brenda Gajelan-Samson

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Eutrophication is a process where in there is a surplus of nutrients present in a lake or river. Harmful cyanobacteria, hypoxia, and primarily algae, which contain toxins, grow because of the excess nutrients. Algal blooms can cause fish kills, limiting the light penetration which reduces growth of aquatic organisms, causing die-offs of plants and produce conditions that are dangerous to aquatic and human life. The main cause for eutrophication is the presence of excessive amounts of phosphorus (P) and nitrogen (N). Nitrogen is necessary for the production of the plant tissues and is usually used to synthesize proteins. Nitrate is a compound that contains nitrogen, and at elevated levels it can cause harmful effects. Excessive amounts of phosphorus, displaced through human activity, is the major cause of algae growth and as well as degraded water quality. To accomplish this study the Assessment of Soluble inorganic nitrogen (SIN), Assessment of Soluble reactive phosphate (SRP), Determination of Chlorophyll a (Chl-a) concentration, and Determination of Dominating Taxa were done. The study addresses the high probability of algal blooms in Maqueda Bay by assessing the biotic and abiotic factors of Antiao and Jiabong rivers. The data predicts the overgrowth of algae and to create awareness to prevent the event from taking place. The study assesses the adverse effects that could be prevented by understanding and controlling algae. This should predict future cases of algal blooms and allow government agencies which require data to create programs to prevent and assess these issues.

Keywords: eutrophication, chlorophyll a, nitrogen, phosphorus, red tide, Kjeldahl method, spectrophotometer, assessment of soluble inorganic nitrogen, SIN, assessment of soluble reactive phosphate, SRP

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

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Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Raimoana Frogier, Luc Girard, Pierre Bauduin, Diane Rebiscoul, Olivier Diat

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Nano-ions (NIs) are ionic species or clusters of nanometric size. Their low charge density and the delocalization of their charges give special properties to some of NIs belonging to chemical classes of polyoxometalates (POMs) or boron clusters. They have the particularity of interacting non-covalently with neutral hydrated surface or interfaces such as assemblies of surface-active molecules (micelles, vesicles, lyotropic liquid crystals), foam bubbles or emulsion droplets. This makes possible to classify those NIs in the Hofmeister series as superchaotropic ions. The mechanism of adsorption is complex, linked to the simultaneous dehydration of the ion and the molecule or supramolecular assembly with which it can interact, all with an enthalpic gain on the free energy of the system. This interaction process is reversible and is sufficiently pronounced to induce changes in molecular and supramolecular shape or conformation, phase transitions in the liquid phase, all at sub-millimolar ionic concentrations. This new property of some NIs opens up new possibilities for applications in fields as varied as biochemistry for solubilization, recovery of metals of interest by foams in the form of NIs... In order to better understand the physico-chemical mechanisms at the origin of this interaction, we use silicon wafers functionalized by non-ionic oligomers (polyethylene glycol chains or PEG) to study in situ by X-ray reflectivity this interaction of NIs with the grafted chains. This study carried out at ESRF (European Synchrotron Radiation Facility) and has shown that the adsorption of the NIs, such as POMs, has a very fast kinetics. Moreover the distribution of the NIs in the grafted PEG chain layer was quantify. These results are very encouraging and confirm what has been observed on soft interfaces such as micelles or foams. The possibility to play on the density, length and chemical nature of the grafted chains makes this system an ideal tool to provide kinetic and thermodynamic information to decipher the complex mechanisms at the origin of this adsorption.

Keywords: adsorption, nano-ions, solid-liquid interface, superchaotropicity

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Authors: Chro Kawyan

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Endothelin-1 (ET-1), the principal individual from the newfound mammalian endothelin group of organically dynamic peptides, was initially distinguished as a 21 buildup powerful vasoconstrictor peptide in vascular endothelial cells. However, it has since been demonstrated to have a wide range of pharmacological activities in tissues both inside and outside the cardiovascular system. Additionally, peptides that have a striking resemblance to ET-1 have been identified as the primary toxic component of snake venom. In addition, late examinations have proposed that warm blooded creatures, including people, produce three unmistakable individuals from this peptide family, ET-1, ET-2 and ET-J, which might have various profiles of organic action and may follow up on particular subtypes of endothelin receptor. Masashi Yanagisawa and Tomoh Masaki survey the ongoing status of the organic chemistry and sub-atomic science of endothelin.

Keywords: thelin, microbiology, molecular biology, cell

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behaviour.

Keywords: seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation

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Authors: Hyelim Park, Juan Martin Zorrilla

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Climate change influences very widely and in various ways ocean ecosystem functioning. The consequences of climate change on marine ecosystems are an increase in temperature and irregular behavior of some solute concentrations. These changes would affect fisheries catches in several ways. Our aim is to assess the quantitative contribution change of fishery catches along the time and express them through four environment variables: Sea Surface Temperature (SST4) and the concentrations of Chlorophyll (CHL), Particulate Inorganic Carbon (PIC) and Particulate Organic Carbon (POC) at two spatial scales: Global and the nineteen FAO Major Fishing Areas divisions. Data collection was based on the FAO FishStatJ 2014 database as well as MODIS Aqua satellite observations from 2002 to 2012. Some data had to be corrected and interpolated using some existing methods. As the results, a multivariable regression model for average Global fisheries captures contained temporal mean of SST4, standard deviation of SST4, standard deviation of CHL and standard deviation of PIC. Global vector auto-regressive (VAR) model showed that SST4 was a statistical cause of global fishery capture. To accommodate varying conditions in fishery condition and influence of climate change variables, a model was constructed for each FAO major fishing area. From the management perspective it should be recognized some limitations of the FAO marine areas division that opens to possibility to the discussion of the subdivision of the areas into smaller units. Furthermore, it should be treated that the contribution changes of fishery species and the possible environment factor for specific species at various scale levels.

Keywords: fisheries-catch, FAO FishStatJ, MODIS Aqua, sea surface temperature (SST), chlorophyll, particulate inorganic carbon (PIC), particulate organic carbon (POC), VAR, granger causality

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Authors: Babak Safaei, A. M. Fattahi

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In the present study we have investigated axial buckling characteristics of nanocomposite beams reinforced by single-walled carbon nanotubes (SWCNTs). Various types of beam theories including Euler-Bernoulli beam theory, Timoshenko beam theory and Reddy beam theory were used to analyze the buckling behavior of carbon nanotube-reinforced composite beams. Generalized differential quadrature (GDQ) method was utilized to discretize the governing differential equations along with four commonly used boundary conditions. The material properties of the nanocomposite beams were obtained using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites which were embedded by amorphous polyethylene matrix. Then the results obtained directly from MD simulations were matched with those calculated by the mixture rule to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results were presented to indicate the influences of nanotube volume fractions and end supports on the critical axial buckling loads of nanocomposite beams relevant to long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, axial buckling, generalized differential quadrature (GDQ)

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Authors: Paromik Bhattacharyya, Vijay Kumar, Johannes Van Staden

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Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

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Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

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Authors: Sukriti Sabharwal, Sonali Bhattar, Shikhar Saxena

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Introduction: COVID-19 molecular diagnostic laboratory is the cornerstone of the COVID-19 disease diagnosis as the patient’s treatment and management protocol depend on the molecular results. For this purpose, it is extremely important that the laboratory conducting these results adheres to the quality management processes to increase the accuracy and validity of the reports generated. We started our own molecular diagnostic setup at the onset of the pandemic. Therefore, we conducted this study to generate our quality management data to help us in improving on our weak points. Materials and Methods: A total of 14561 samples were evaluated by the retrospective observational method. The quality variables analysed were classified into pre-analytical, analytical, and post-analytical variables, and the results were presented in percentages. Results: Among the pre-analytical variables, sample leaking was the most common cause of the rejection of samples (134/14561, 0.92%), followed by non-generation of SRF ID (76/14561, 0.52%) and non-compliance to triple packaging (44/14561, 0.3%). The other pre-analytical aspects assessed were incomplete patient identification (17/14561, 0.11%), insufficient quantity of samples (12/14561, 0.08%), missing forms/samples (7/14561, 0.04%), samples in the wrong vials/empty VTM tubes (5/14561, 0.03%) and LIMS entry not done (2/14561, 0.01%). We are unable to obtain internal quality control in 0.37% of samples (55/14561). We also experienced two incidences of cross-contamination among the samples resulting in false-positive results. Among the post-analytical factors, a total of 0.07% of samples (11/14561) could not be dispatched within the stipulated time frame. Conclusion: Adherence to quality control processes is foremost for the smooth running of any diagnostic laboratory, especially the ones involved in critical reporting. Not only do the indicators help in keeping in check the laboratory parameters but they also allow comparison with other laboratories.

Keywords: laboratory quality management, COVID-19, molecular diagnostics, healthcare

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Authors: W. S. Mohamed, A. A. Hammam

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Sandy soils under arid and semi-arid conditions are characterized by poor physical and biochemical properties such as low water retention, rapid organic matter decomposition, low nutrients use efficiency, and limited crop productivity. Addition of organic amendments is crucial to develop soil properties and consequently enhance nutrients use efficiency and lessen organic carbon decomposition. Two years field experiments were developed to investigate the feasibility of using poultry manure and its derived biochar integrated with different levels of N fertilizer as a soil amendment for newly reclaimed sandy soils in Western Desert of El-Minia Governorate, Egypt. Results of this research revealed that poultry manure and its derived biochar addition induced pronounced effects on soil moisture content at saturation point, field capacity (FC) and consequently available water. Data showed that application of poultry manure (PM) or PM-derived biochar (PMB) in combination with inorganic N levels had caused significant changes on a range of the investigated sandy soil biochemical properties including pH, EC, mineral N, dissolved organic carbon (DOC), dissolved organic N (DON) and quotient DOC/DON. Overall, the impact of PMB on soil physical properties was detected to be superior than the impact of PM, regardless the inorganic N levels. In addition, the obtained results showed that PM and PM application had the capacity to stimulate vigorous growth, nutritional status, production levels of wheat and sorghum, and to increase soil organic matter content and N uptake and recovery compared to control. By contrast, comparing between PM and PMB at different levels of inorganic N, the obtained results showed higher relative increases in both grain and straw yields of wheat in plots treated with PM than in those treated with PMB. The interesting feature of this research is that the biochar derived from PM increased treated sandy soil organic carbon (SOC) 1.75 times more than soil treated with PM itself at the end of cropping seasons albeit double-applied amount of PM. This was attributed to the higher carbon stability of biochar treated sandy soils increasing soil persistence for carbon decomposition in comparison with PM labile carbon. It could be concluded that organic manures applied to sandy soils under arid and semi-arid conditions are subjected to high decomposition and mineralization rates through crop seasons. Biochar derived from organic wastes considers as a source of stable carbon and could be very hopeful choice for substituting easily decomposable organic manures under arid conditions. Therefore, sustainable agriculture and productivity in newly reclaimed sandy soils desire one high rate addition of biochar derived from organic manures instead of frequent addition of such organic amendments.

Keywords: biochar, dissolved organic carbon, N-uptake, poultry, sandy soil

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Authors: Ghazanfar Ali, Fahad N Almajhdi

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This study provides data on the viral diagnosis and molecular epidemiology of influenza A(H3N2) virus isolated in Riyadh, Saudi Arabia. Nasopharyngeal aspirates from 80 clinically infected patients in the peak of the 2010-2011 winter seasons were processed for viral diagnosis by RT-PCR. Sequencing of entire HA and NA genes of representative isolates and molecular epidemiological analysis were performed. A total of 06 patients were positive for influenza A, B and respiratory syncytial viruses by RT-PCR assays; out of these only one sample was positive for influenza A(H3N2) by RT-PCR. Phylogenetic analysis of the HA and NA gene sequences showed identities higher than 99-98.8 % in both genes. They were also similar to reference isolates in HA sequences (99 % identity) and in NA sequences (99 % identity). Amino acid sequences predicted for the HA gene were highly identical to reference strains. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. Conclusion: Viral isolation and RT-PCR together were useful for diagnosis of the influenza A (H3N2) virus. Variations in HA and NA sequences are similar to those identified in worldwide reference isolates and no drug resistance was found.

Keywords: influenza A (H3N2), genetic characterization, viral isolation, RT-PCR, Saudi Arabia

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Authors: Leila Momenzadeh, Alexander V. Evteev, Elena V. Levchenko, Tanvir Ahmed, Irina Belova, Graeme Murch

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In this work, the phonon thermal conductivity of f.c.c. Al is investigated in detail in the temperature range 100 – 900 K within the framework of equilibrium molecular dynamics simulations making use of the Green-Kubo formalism and one of the most reliable embedded-atom method potentials. It is found that the heat current auto-correlation function of the f.c.c. Al model demonstrates a two-stage temporal decay similar to the previously observed for f.c.c Cu model. After the first stage of decay, the heat current auto-correlation function of the f.c.c. Al model demonstrates a peak in the temperature range 100-800 K. The intensity of the peak decreases as the temperature increases. At 900 K, it transforms to a shoulder. To describe the observed two-stage decay of the heat current auto-correlation function of the f.c.c. Al model, we employ decomposition model recently developed for phonon-mediated thermal transport in a monoatomic lattice. We found that the electronic contribution to the total thermal conductivity of f.c.c. Al dominates over the whole studied temperature range. However, the phonon contribution to the total thermal conductivity of f.c.c. Al increases as temperature decreases. It is about 1.05% at 900 K and about 12.5% at 100 K.

Keywords: aluminum, gGreen-Kubo formalism, molecular dynamics, phonon thermal conductivity

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Authors: Reema K. AlEssa, Sahar Alshomer, Abdullah Alfaleh, Sultan ALkhenaizan, Mohammed Albalwi

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Ichthyosis is a disorder of abnormal keratinization, characterized by excessive scaling, and consists of more than twenty subtypes varied in severity, mode of inheritance, and the genes involved. There is insufficient data in the literature about the epidemiology and characteristics of ichthyosis locally. Our aim is to identify the histopathological features and genetic profile of ichthyosis. Method: It is an observational retrospective case series study conducted in March 2020, included all patients who were diagnosed with Ichthyosis and confirmed by histological and molecular findings over the last 20 years in King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. Molecular analysis was performed by testing genomic DNA and checking genetic variations using the AmpliSeq panel. All disease-causing variants were checked against HGMD, ClinVar, Genome Aggregation Database (gnomAD), and Exome Aggregation Consortium (ExAC) databases. Result: A total of 60 cases of Ichthyosis were identified with a mean age of 13 ± 9.2. There is an almost equal distribution between female patients 29 (48%) and males 31 (52%). The majority of them were Saudis, 94%. More than half of patients presented with general scaling 33 (55%), followed by dryness and coarse skin 19 (31.6%) and hyperlinearity 5 (8.33%). Family history and history of consanguinity were seen in 26 (43.3% ), 13 (22%), respectively. History of colloidal babies was found in 6 (10%) cases of ichthyosis. The most frequent genes were ALOX12B, ALOXE3, CERS3, CYP4F22, DOLK, FLG2, GJB2, PNPLA1, SLC27A4, SPINK5, STS, SUMF1, TGM1, TGM5, VPS33B. Most frequent variations were detected in CYP4F22 in 16 cases (26.6%) followed by ALOXE3 6 (10%) and STS 6 (10%) then TGM1 5 (8.3) and ALOX12B 5 (8.3). The analysis of molecular genetic identified 23 different genetic variations in the genes of ichthyosis, of which 13 were novel mutations. Homozygous mutations were detected in the majority of ichthyosis cases, 54 (90%), and only 1 case was heterozygous. Few cases, 4 (6.6%) had an unknown type of ichthyosis with a negative genetic result. Conclusion: 13 novel mutations were discovered. Also, about half of ichthyosis patients had a positive history of consanguinity.

Keywords: ichthyosis, genetic profile, molecular characterization, congenital ichthyosis

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Authors: Raj Kishore Swain, Kamdev Sethy, Sumanta Kumar Mishra

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Selenium is an essential trace element for the chicken with a variety of biological functions like growth, fertility, immune system, hormone metabolism, and antioxidant defense systems. Selenium deficiency in chicken causes exudative diathesis, pancreatic dystrophy and nutritional muscle dystrophy of the gizzard, heart and skeletal muscle. Additionally, insufficient immunity, lowering of production ability, decreased feathering of chickens and increased embryo mortality may occur due to selenium deficiency. Nano elemental selenium, which is bright red, highly stable, soluble and of nano meter size in the redox state of zero, has high bioavailability and low toxicity due to the greater surface area, high surface activity, high catalytic efficiency and strong adsorbing ability. To assess the effect of dietary nano-Se on performance and expression of gene in Vencobb broiler birds in comparison to its inorganic form (sodium selenite), four hundred fifty day-old Vencobb broiler chicks were randomly distributed into 9 dietary treatment groups with two replicates with 25 chicks per replicate. The dietary treatments were: T1 (Control group): Basal diet; T2: Basal diet with 0.3 ppm of inorganic Se; T3: Basal diet with 0.01875 ppm of nano-Se; T4: Basal diet with 0.0375 ppm of nano-Se; T5: Basal diet with 0.075 ppm of nano-Se, T6: Basal diet with 0.15 ppm of nano-Se, T7: Basal diet with 0.3 ppm of nano-Se, T8: Basal diet with 0.60 ppm of nano-Se, T9: Basal diet with 1.20 ppm of nano-Se. Nano selenium was synthesized by mixing sodium selenite with reduced glutathione and bovine serum albumin. The experiment was carried out in two phases: starter phase (0-3 wks), finisher phase (4-5 wk) in deep litter system. The body weight at the 5th week was best observed in T4. The best feed conversion ratio at the end of 5th week was observed in T4. Erythrocytic catalase, glutathione peroxidase and superoxide dismutase activity were significantly (P < 0.05) higher in all the nano selenium treated groups at 5th week. The antibody titers (log2) against Ranikhet diseases vaccine immunization of 5th-week broiler birds were significantly higher (P < 0.05) in the treatments T4 to T7. The selenium levels in liver, breast, kidney, brain, and gizzard were significantly (P < 0.05) increased with increasing dietary nano-Se indicating higher bioavailability of nano-Se compared to inorganic Se. The real time polymer chain reaction analysis showed an increase in the expression of antioxidative gene in T4 and T7 group. Therefore, it is concluded that supplementation of nano-selenium at 0.0375 ppm over and above the basal level can improve the body weight, antioxidant enzyme activity, Se bioavailability and expression of the antioxidative gene in broiler birds.

Keywords: chicken, growth, immunity, nano selenium

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Authors: Soniya Chaudhary, Sanjeev Sahu

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Propagation of Rayleigh-type waves in a rotating piezoelectric plate is investigated. The materials are assumed to be transversely isotropic crystals. The frequency equation have been derived for electrically open and short cases. Effect of rotation and piezoelectricity have been shown. It is also found that piezoelectric material properties have an important effect on Rayleigh wave propagation. The result is relevant to the analysis and design of various acoustic surface wave devices constructed from piezoelectric materials also in SAW devices.

Keywords: rotation, frequency equation, piezoelectricity, rayleigh-type wave

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Authors: Amanda M. Tadini, Houssam Hajjoul, Gustavo Nicolodelli, Stéphane Mounier, Célia R. Montes, Débora M. B. P. Milori

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Soil organic matter (SOM) plays an important role in maintaining soil productivity and accounting for the promotion of biological diversity. The main components of the SOM are the humic substances which can be fractionated according to its solubility in humic acid (HA), fulvic acids (FA) and humin (HU). The determination of the chemical properties of organic matter as well as its interaction with metallic species is an important tool for understanding the structure of the humic fractions. Fluorescence spectroscopy has been studied as a source of information about what is happening at the molecular level in these compounds. Specially, soils of Amazon region are an important ecosystem of the planet. The aim of this study is to understand the molecular and structural composition of HA samples from Spodosol of Amazonia using the fluorescence Emission-Excitation Matrix (EEM) and Time Resolved Fluorescence Spectroscopy (TRFS). The results showed that the samples of HA showed two fluorescent components; one has a more complex structure and the other one has a simpler structure, which was also seen in TRFS through the evaluation of each sample lifetime. Thus, studies of this nature become important because it aims to evaluate the molecular and structural characteristics of the humic fractions in the region that is considered as one of the most important regions in the world, the Amazon.

Keywords: Amazonian soil, characterization, fluorescence, humic acid, lifetime

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Authors: Desouky Abd El Haleem, Sahar Zaki

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This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Determination of the behavior of clathrate hydrate with inhibitor in the THz region will provide useful information about hydrate plug control in the upstream of the oil and gas industry. In this study, terahertz time-domain spectroscopy (THz-TDS) revealed the inhibition of the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different molecular weights. Distinct footprints of phase transition in the THz region (0.4–2.2 THz) were analyzed and absorption coefficients and real part of refractive indices are obtained in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz spectroscopy, tetrahydrofuran, inhibitor

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Authors: Seyedmajid Mehrnia, Maximilan Kuhr, Peter F. Pelz

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Molecular Dynamics (MD) simulation is a proven method to inspect behaviours of lubricant oils in nano-scale gaps. However, most MD simulations on tribology have been performed with atomically smooth walls to determine wall slip and friction properties. This study will investigate the effect of porosity, specifically nano-porous walls, on wall slip properties of hydrocarbon oils confined between two walls in a Couette flow. Different pore geometries will be modelled to investigate the effect on wall slip and bulk shear. In this paper, the Polyalphaolefin (PAO) molecules are confined to a stationary and a moving wall. A hybrid force field consisting of different potential energy functions was employed in this MD simulation. Newton’s law defines how those forces will influence the atoms' movements. The interactions among surface atoms were simulated with an Embedded Atom Method (EAM) potential function which can represent the characteristics of metallic arrangements very strongly. We implemented NERD forcefield for intramolecular potential energy function. Also, Lennard-Jones potential was employed for nonbonded intermolecular interaction.

Keywords: slip length, molecular dynamics, critical shear rate, Couette flow

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Authors: Kayode Fatokun, Nozipho N. Motsa

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Field experiments were carried out during the summer/autumn (first trial) and winter/spring (second trial) seasons of 2019 and 2021 inDlangubo, Ngwelezane, and Mtubatubaareas of KwaZulu-Natal Province of South Africa to study the drought amelioration effects and impact of 2 locally available organic wastes [filter cake (FC) and macadamia husk compost (MHC)] on the productivity, and physiological responses of 4 orange-fleshed sweet potato cultivars (Buregard cv., Impilo, W-119 and 199062.1). The effects of FC and MHC were compared with that of inorganic fertilizer (IF) [2:3:2 (30)], FC+IF, MHC+IF, and control. The soil amendments were applied in the first trials only. Climatic data such as humidity, temperature, and rainfall were taken via remote sensing. The results of the first trial indicated that filter cake and IF significantly performed better than MHC. While the strength of filter cake may be attributable to its rich array of mineral nutrients such as calcium, magnesium, potassium, sodium, zinc, copper, manganese, iron, and phosphorus. The little performance from MHC may be attributable to its water holding capacity. Also, a positive correction occurred between the yield of the test OFSP cultivars and climatic factors such as rainfall, NDVI, and NDWI values. Whereas the inorganic fertilizer did not have any significant effect on the growth and productivity of any of the tested sweet potato cultivars in the second trial; FC, and MHC largely maintained their significant performances. In conclusion, the use of FC is highly recommended in the production of the test orange-fleshed sweet potato cultivars. Also, the study indicated that both FC and MHC may not only supply the needed plant nutrients but has the capacity to reduce the impact of drought on the growth of the test cultivars. These findings are of great value to farmers, especially the resource-poorones.

Keywords: amendments, drought, filter cake, macadamia husk compost, sweet potato

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Authors: Syed Asif Hassan, Syed Atif Hassan

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Multidrug-resistant Tuberculosis (MDR-TB) is an infection caused by the resistant strains of Mycobacterium tuberculosis that do not respond either to isoniazid or rifampicin, which are the most important anti-TB drugs. The increase in the occurrence of a drug-resistance strain of MTB calls for an intensive search of novel target-based therapeutics. In this context LprG (Rv1411c) a lipoprotein from MTB plays a pivotal role in the immune evasion of Mtb leading to survival and propagation of the bacterium within the host cell. Therefore, a machine learning method will be developed for generating a computational model that could predict for a potential anti LprG activity of the novel antituberculosis compound. The present study will utilize dataset from PubChem database maintained by National Center for Biotechnology Information (NCBI). The dataset involves compounds screened against MTB were categorized as active and inactive based upon PubChem activity score. PowerMV, a molecular descriptor generator, and visualization tool will be used to generate the 2D molecular descriptors for the actives and inactive compounds present in the dataset. The 2D molecular descriptors generated from PowerMV will be used as features. We feed these features into three different classifiers, namely, random forest, a deep neural network, and a recurring neural network, to build separate predictive models and choosing the best performing model based on the accuracy of predicting novel antituberculosis compound with an anti LprG activity. Additionally, the efficacy of predicted active compounds will be screened using SMARTS filter to choose molecule with drug-like features.

Keywords: antituberculosis drug, classifier, machine learning, molecular descriptors, prediction

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Surrogate model has received increasing attention for use in detecting damage of structures based on vibration modal parameters. However, uncertainties existing in the measured vibration data may lead to false or unreliable output result from such model. In this study, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The kriging technique allows one to genuinely quantify the surrogate error, therefore it is chosen as metamodeling technique. Enhanced version of ideal gas molecular movement (EIGMM) algorithm is used as main algorithm for model updating. The developed approach is applied to detect simulated damage in numerical models of 72-bar space truss and 120-bar dome truss. The simulation results show the proposed method can perform well in probability-based damage detection of structures with less computational effort compared to direct finite element model.

Keywords: probability-based damage detection (PBDD), Kriging, surrogate modeling, uncertainty quantification, artificial intelligence, enhanced ideal gas molecular movement (EIGMM)

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Authors: Rachel Danielson, Brendan Bohannan, S.M. Tsai, Kyle Meyer, Jorge L.M. Rodrigues

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The Amazon Rainforest is a global diversity hotspot and crucial carbon sink, but approximately 20% of its total extent has been deforested- primarily for the establishment of cattle pasture. Understanding the impact of this large-scale disturbance on soil microbial community composition and activity is crucial in understanding potentially consequential shifts in nutrient or greenhouse gas cycling, as well as adding to the body of knowledge concerning how these complex communities respond to human disturbance. In this study, surface soils (0-10cm) were collected from three forests and three 45-year-old pastures in Rondonia, Brazil (the Amazon state with the greatest rate of forest destruction) in order to determine the impact of forest conversion on microbial communities involved in nitrogen fixation. Soil chemical and physical parameters were paired with measurements of microbial activity and genetic profiles to determine how community composition and process rates relate to environmental conditions. Measuring both the natural abundance of 15N in total soil N, as well as incorporation of enriched 15N2 under incubation has revealed that conversion of primary forest to cattle pasture results in a significant increase in the rate of nitrogen fixation by free-living diazotrophs. Quantification of nifH gene copy numbers (an essential subunit encoding the nitrogenase enzyme) correspondingly reveals a significant increase of genes in pasture compared to forest soils. Additionally, genetic sequencing of both nifH genes and transcripts shows a significant increase in the diversity of the present and metabolically active diazotrophs within the soil community. Levels of both organic and inorganic nitrogen tend to be lower in pastures compared to forests, with ammonium rather than nitrate as the dominant inorganic form. However, no significant or consistent differences in total, extractable, permanganate-oxidizable, or loss-on-ignition carbon are present between the two land-use types. Forest conversion is associated with a 0.5- 1.0 unit pH increase, but concentrations of many biologically relevant nutrients such as phosphorus do not increase consistently. Increases in free-living diazotrophic community abundance and activity appear to be related to shifts in carbon to nitrogen pool ratios. Furthermore, there may be an important impact of transient, low molecular weight plant-root-derived organic carbon on free-living diazotroph communities not captured in this study. Preliminary analysis of nitrogenase gene variant composition using NovoSeq metagenomic sequencing indicates that conversion of forest to pasture may significantly enrich vanadium-based nitrogenases. This indication is complemented by a significant decrease in available soil molybdenum. Very little is known about the ecology of diazotrophs utilizing vanadium-based nitrogenases, so further analysis may reveal important environmental conditions favoring their abundance and diversity in soil systems. Taken together, the results of this study indicate a significant change in nitrogen cycling and diazotroph community composition with the conversion of the Amazon Rainforest. This may have important implications for the sustainability of cattle pastures once established since nitrogen is a crucial nutrient for forage grass productivity.

Keywords: free-living diazotrophs, land use change, metagenomic sequencing, nitrogen fixation

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Authors: Hamid Khachab, Yamani Abdelkafi, Mouna Barhmi

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The epitaxial growth has great important in the fabricate of the new semi-conductors devices and upgrading many factors, such as the quality of crystallization and efficiency with their deferent types and the most effective epitaxial technique is the molecular beam epitaxial. The MBE growth modeling allows to confirm the experiments results out by atomic beam and to analyze the microscopic phenomena. In of our work, we determined the growth processes specially the ZnSe epitaxial technique by Kinetic Monte Carlo method and we also give observations that are made in real time at the growth temperature using reflection high energy electron diffraction (RHEED) and photoemission current.

Keywords: molecular beam epitaxy, II-VI, morpholy, photoemission, RHEED, simulation, kinetic Monte Carlo, ZnSe

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Authors: Meryem Imane Babaghayou, Abdelhafidi Asma

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This study deals with the ageing of Blown extruded films of low-density polyethylene (LDPE), used for greenhouse covering. The LDPE have been subjected to climatic ageing in a sub-Saharan facility at Laghouat (Algeria) with direct exposure to sun. The microstructural changes in the films were analyzed by IRFT for different states of ageing. The mechanical characterization was performed on a uniaxial tensile apparatus. The mechanical properties such as Young's modulus, strain at break, and stress at break have been followed for different states of exposure time (0 to 6 months). The Climatic ageing of LDPE films shows the effect of ageing on the microstructural Plan which leads to: i) To an oxidation of the molecular chains. ii) To the formation of cross-linkings and breaking chains, which both of them are responsible for the mechanical behavior’s modifications of the material. Cross-links are in favor of strengthening of the mechanical properties at break (the increase of σr and εr). In other side, the chains breaking leads to a decrease of these properties. The increase in the Young's modulus also seems to be related to those structural changes since the cross-links increase the average molecular weight. Branchings and tangles are favorable pairs for the ductile nature of the material. And in other side, the chains breaking reduces the average molecular weight and therefore promotes the stiffening (following to morphological changes) so the material becomes fragile. The post-mortem analysis of the samples shows that the mechanical stress has an effect on the molecular structure of the material. Although if quantitatively the concentrations of different chemical species exchanges, from a quantitative point of view only the unsaturations raises the polemics of a possible microstructural modification induced by mechanical stress applied during the tensile test. Also, we recommend a more rigorous analysis with other means of investigation.

Keywords: low-density polyethylene, ageing, mechanical properties, IRTF

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

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Authors: Yuanhao Chang, Senbo Xiao, Zhiliang Zhang, Jianying He

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The role of nanoparticles (NPs) in enhanced oil recovery (EOR) is being increasingly emphasized. In this study, the motion of NPs and local stress distribution of tapped oil droplet/nanofluid in nanochannels are studied with coarse-grained modeling and molecular dynamic simulations. The results illustrate three motion patterns for NPs: hydrophilic NPs are more likely to adsorb on the channel and stay near the three-phase contact areas, hydrophobic NPs move inside the oil droplet as clusters and more mixed NPs are trapped at the oil-water interface. NPs in each pattern affect the flow of fluid and the interfacial thickness to various degrees. Based on the calculation of atomistic stress, the characteristic that the higher value of stress occurs at the place where NPs aggregate can be obtained. Different occurrence patterns correspond to specific local stress distribution. Significantly, in the three-phase contact area for hydrophilic NPs, the local stress distribution close to the pattern of structural disjoining pressure is observed, which proves the existence of structural disjoining pressure in molecular dynamics simulation for the first time. Our results guide the design and screen of NPs for EOR and provide a basic understanding of nanofluid applications.

Keywords: local stress distribution, nanoparticles, enhanced oil recovery, molecular dynamics simulation, trapped oil droplet, structural disjoining pressure

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Authors: D. A. S. Gamage, B. F. A. Basnayake, W. A. J. M. De Costa

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Agriculture plays an important and strategic role in the performance of Sri Lankan national economy. Rice is the staple food of Sri Lankans thus; rice cultivation is the major agricultural activity of the country. In Sri Lanka, out of the total rice production, a considerable amount of rice straw and rice husk goes wasted. Hence, there is a great potential of production of quality compost and rice husk charcoal. The concept of making rice straw compost and rice husk charcoal is practicable in Sri Lanka, where more than 40% of the farmers are engaged in rice cultivation. The application of inorganic nitrogen fertilizer has become a burden to the country. Rice husk charcoal as a coating material to retain N fertilizer is a suitable solution to gradually release nitrogenous compounds. Objective of this study was to produce rice husk charcoal coated urea as a slow releasing fertilizer with rice straw compost and to compare the leaching losses of nitrogen, phosphorus and potassium using leaching columns. Leaching column studies were prepared using 1.2 m tall PVC pipes with a diameter of 15 cm and a sampling port was attached to the bottom end of the column-cap. Leachates (100 ml/leaching column) were obtained from two sets of (each set has four leaching columns) leaching columns. The sampling was done once a week for 3 month period. Rice husk charcoal coated urea can potentially be used as a slow releasing nitrogen fertilizer which reduces leaching losses of urea. It also helps reduce the phosphate and potassium leaching. The cyclic effect of phosphate release is an important finding which could be the central issue in defining microbial behavior in soils. The fluctuations of phosphate may have cyclic effects of 28 days. In addition, rice straw compost and rice husk charcoal coating is less costly and contribute to mitigate pollution of water bodies by inorganic fertilizers.

Keywords: leaching, mitigate, rice husk charcoal, slow releasing fertilizer

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Authors: Misbah Khan, Jian Wen, Muhammad Asif Shakoori

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The Organic Rankine Cycle (ORC) plays an important role in converting low-temperature heat sources into electrical power by using refrigerants as working fluids. The thermophysical properties of working fluids are essential for designing ORC. HFO-1336mzz(Z) (cis-1,1,1,4,4,4-hexafluoro-2-butene) considered as working fluid and have almost 99% low GWP and relatively same thermophysical properties used as a replacement of HFC-245fa (1,1,1,3,3-pentafluoro-propane). The environmental, safety, healthy and thermophysical properties of HFO-1336mzz(Z) are needed to use it in a practical system. In this paper, Molecular dynamics simulations were used to investigate the Homogeneous condensation, thermophysical and structural properties of HFO-1336mzz(Z) and HFC-245fa. The effect of various temperatures and pressures on thermophysical properties and condensation was extensively investigated. The liquid densities and isobaric heat capacities of this refrigerant was simulated at 273.15K to 353.15K temperatures and pressure0.5-4.0MPa. The simulation outcomes were compared with experimental data to validate our simulation method. The mean square displacement for different temperatures was investigated for dynamical analysis. The variations in potential energies and condensation rate were simulated to get insight into the condensation process. The radial distribution function was simulated at the micro level for structural analysis and revealed that the phase transition of HFO-1336mzz(Z) did not affect the intramolecular structure.

Keywords: homogenous condensation, refrigerants, molecular dynamics simulations, organic rankine cycle

Procedia PDF Downloads 137