Search results for: molecular profiles

Authors: M. Jonathan D. Morales, R. Ramón Silva

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The purpose of this project is to carry out an analysis and determine the profile of actual lean manufacturing processes in the Metropolitan Area of Bucaramanga. Through the analysis of qualitative and quantitative variables it was possible to establish how these manufacturers develop production practices that ensure their competitiveness and productivity in the market. In this study, a random sample of metallurgic and wrought iron companies was applied, following which a quantitative focus and analysis was used to formulate a qualitative methodology for measuring the level of lean manufacturing procedures in the industry. A qualitative evaluation was also carried out through a multivariate analysis using the Numerical Taxonomy System (NTSYS) program which should allow for the determination of Lean Manufacturing profiles. Through the results it was possible to observe how the companies in the sector are doing with respect to Lean Manufacturing Practices, as well as identify the level of management that these companies practice with respect to this topic. In addition, it was possible to ascertain that there is no one dominant profile in the sector when it comes to Lean Manufacturing. It was established that the companies in the metallurgic and wrought iron industry show low levels of Lean Manufacturing implementation. Each one carries out diverse actions that are insufficient to consolidate a sectoral strategy for developing a competitive advantage which enables them to tie together a production strategy.

Keywords: production line management, metallurgic industry, lean manufacturing, productivity

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Authors: O. E. Okafor, L. U. S. Ezeanyika, C. G. Nkwonta, C. J. Okonkwo

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The effect of processing on plasma lipid profile and atherogenic indices of rats fed Artocarpus heterophyllus seed diets at different concentrations were investigated. Fifty five rats were used for this study, they were divided into eleven groups of five rats each (one control group and ten test groups), the test groups were fed raw, boiled, roasted, fermented, and soaked diets at 10 % and 40% concentrations. The study lasted for thirty five days. The diets led to significant decrease (p < 0.05) in plasma cholesterol and triacylglycerol of rats fed 10% and 40% concentrations of the diets, and a significant increase (p < 0.05) in high density lipoprotein (HDL) levels at 40% concentrations of the test diets. The diets also produced decrease in low density lipoprotein (LDL), very low density lipoprotein (VLDL), cardiac risk ratio (CRR), atherogenic index of plasma (AIP) and atherogenic coefficient (AC) at 40% concentrations except the soaked group that showed slight elevation of LDL, CRR, AC and AIP at 40% concentration. Artocarpus heterophyllus seeds could be beneficial to health because of its ability to increase plasma HDL and reduce plasma LDL, VLDL, cholesterol, triglycerides and atherogenic indices at higher diet concentration.

Keywords: artocarpus heterophyllus, atherogenic indices, concentrations, lipid profile

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Authors: Hsiang-Ru Lin

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Cholesterol plays an essential role in the regulation of the progression of numerous important diseases including atherosclerosis and Alzheimer disease so the generation of suitable cholesterol-lowering reagents is urgent to develop. Liver X receptor (LXR) is a ligand-activated transcription factor whose natural ligands are cholesterols, oxysterols and glucose. Once being activated, LXR can transactivate the transcription action of various genes including CYP7A1, ABCA1, and SREBP1c, involved in the lipid metabolism, glucose metabolism and inflammatory pathway. Essentially, the upregulation of ABCA1 facilitates cholesterol efflux from the cells and attenuates the production of beta-amyloid (ABeta) 42 in brain so LXR is a promising target to develop the cholesterol-lowering reagents and preventative treatment of Alzheimer disease. Engelhardia roxburghiana is a deciduous tree growing in India, China, and Taiwan. However, its chemical composition is only reported to exhibit antitubercular and anti-inflammatory effects. In this study, four compounds, engelheptanoxides A, C, engelhardiol A, and B isolated from the root of Engelhardia roxburghiana were evaluated for their agonistic activity against LXR by the transient transfection reporter assays in the HepG2 cells. Furthermore, their interactive modes with LXR ligand binding pocket were generated by molecular modeling programs. By using the cell-based biological assays, engelheptanoxides A, C, engelhardiol A, and B showing no cytotoxic effect against the proliferation of HepG2 cells, exerted obvious LXR agonistic effects with similar activity as T0901317, a novel synthetic LXR agonist. Further modeling studies including docking and SAR (structure-activity relationship) showed that these compounds can locate in LXR ligand binding pocket in the similar manner as T0901317. Thus, LXR is one of nuclear receptors targeted by pharmaceutical industry for developing treatments of Alzheimer and atherosclerosis diseases. Importantly, the cell-based assays, together with molecular modeling studies suggesting a plausible binding mode, demonstrate that engelheptanoxides A, C, engelhardiol A, and B function as LXR agonists. This is the first report to demonstrate that the extract of Engelhardia roxburghiana contains LXR agonists. As such, these active components of Engelhardia roxburghiana or subsequent analogs may show important therapeutic effects through selective modulation of the LXR pathway.

Keywords: Liver X receptor (LXR), Engelhardia roxburghiana, CYP7A1, ABCA1, SREBP1c, HepG2 cells

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Authors: Marium Shaikh, Tahira M. Ali, Abid Hasnain

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Physical and sensory properties of white sauces prepared from native and chemically modified corn and pearl millet starches were compared. Interestingly, no syneresis was observed in hydroxypropylated corn and pearl millet starch containing white sauce even after nine days of cold storage (4 °C), while other modifications also reduced the syneresis significantly in comparison to their native counterparts. White sauce containing succinylated corn starch showed least oil separation due to its greater emulsion stability. Light microscopy was used to visualize the size and shape of fat globules, and it was found that they were most homogenously distributed in succinylated and hydroxypropylated samples. Sensory results revealed that chemical modification of corn and pearl millet starch improved the consistency, thickness and overall acceptability of white sauces. Viscosity profiles showed that pasting parameters of native pearl millet starch are almost similar to native corn starch suggesting pearl millet starch as an alternative of corn starch. Also, white sauce prepared from modified pearl millet starch showed better cold storage stability in terms of various textural attributes like hardness, cohesiveness, chewiness, and springiness.

Keywords: corn starch, pearl millet, hydroxypropylation, succinylation, white sauce

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Authors: Ming-Yen Chang, Sheng-Hung Ke

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This research focuses on the development of a speed bump identification system for real-time control of adjustable shock absorbers in vehicular suspension systems. The study initially involved the collection of images of various speed bumps, and rubber speed bump profiles found on roadways. These images were utilized for training and recognition purposes through the deep learning object detection algorithm YOLOv5. Subsequently, the trained speed bump identification program was integrated with an in-vehicle camera system for live image capture during driving. These images were instantly transmitted to a computer for processing. Using the principles of monocular vision ranging, the distance between the vehicle and an approaching speed bump was determined. The appropriate control distance was established through both practical vehicle measurements and theoretical calculations. Collaboratively, with the electronically adjustable shock absorbers equipped in the vehicle, a shock absorber control system was devised to dynamically adapt the damping force just prior to encountering a speed bump. This system effectively mitigates passenger discomfort and enhances ride quality.

Keywords: adjustable shock absorbers, image recognition, monocular vision ranging, ride

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Authors: Rafik Baouche, Rabah Chaouchi

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This work reports the first comprehensive stress field interpretation from the eleven recently drilled wells in the Berkaoui Basin, Algerian Sahara. A cumulative length of 7000+m acoustic image logs from 06 vertical wells were investigated, and a mean NW-SE (128°-145° N) maximum horizontal stress (SHMax) orientation is inferred from the B-D quality wellbore breakouts. The study integrates log-based approach with the downhole measurements to infer pore pressure, in-situ stress magnitudes. Vertical stress (Sv), interpreted from the bulk-density profiles, has an average gradient of 22.36 MPa/km. The Ordovician and Cambrian reservoirs have a pore pressure gradient of 13.47-13.77 MPa/km, which is more than the hydrostatic pressure regime. A 17.2-18.3 MPa/km gradient of minimum horizontal stress (Shmin) is inferred from the fracture closure pressure in the reservoirs. Breakout widths constrained the SHMax magnitude in the 23.8-26.5 MPa/km range. Subsurface stress distribution in the central Saharan Algeria indicates that the present-day stress field in the Berkaoui Basin is principally strike-slip faulting (SHMax > Sv > Shmin). Inferences are drawn on the regional stress pattern and drilling and reservoir development.

Keywords: stress, imagery, breakouts, sahara

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Authors: Nermin Gozukirmizi, Buket Cakmak, Sevgi Marakli

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Sireviruses are genera of copia LTR retrotransposons with a unique genome structure among retrotransposons. Barley (Hordeum vulgare L.) is an economically important plant and has been studied as a model plant regarding its short annual life cycle and seven chromosome pairs. In this study, we used mature barley embryos, 10-day-old roots and 10-day-old leaves derived from the same barley plant to investigate SIRE1 retrotransposon movements by Inter-Retrotransposon Amplified Polymorphism (IRAP) technique. We found polymorphism rates between 0-64% among embryos, roots and leaves. Polymorphism rates were detected to be 0-27% among embryos, 8-60% among roots, and 11-50% among leaves. Polymorphisms were observed not only among the parts of different individuals, but also on the parts of the same plant (23-64%). The internal domains of SIRE1 (gag, env and rt) were also analyzed in the embryos, roots and leaves. Analysis of band profiles showed no polymorphism for gag, however, different band patterns were observed among samples for rt and env. The sequencing of SIRE1 gag, env and rt domains revealed 79% similarity for gag, 95% for env and 84% for rt to Ty1-copia retrotransposons. SIRE1 retrotransposon was identified in the soybean genome and has been studied on other plants (maize, rice, tomatoe etc.). This study is the first detailed investigation of SIRE1 in barley genome. The obtained findings are expected to contribute to the comprehension of SIRE1 retrotransposon and its role in barley genome.

Keywords: barley, polymorphism, retrotransposon, SIRE1 virus

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Authors: Daseul Lee, Jeong Jun Lee, Ok-Sang Jung

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Self-assembly of a series of ZnX2 (X- = Cl-, Br-, and I-) with 2,3-bis(4’-nicotinamidephenoxy)naphthalene (L) as a new bidentate pyridyl-donor ligand yields systematic metallacyclodimeric unit, [ZnX2L]2. The supramolecule constitutes a characteristically stacked forming both 1D suprachannels and cages. Weak C-H⋯π and inter-digitated π⋯π interactions are main driving forces in the formation of both suprachannels and cages. The slightly different features between the suprachannel and cage have been investigated by 1H NMR and TG analysis, which solvent quantitatively exchange within only suprachannels. Photo-unstable CH2I2 molecules are stabilized via capturing within suprachannels, which is monitored by UV-Vis spectroscopy. Furthermore, the photoluminescence intensity, from the chromophore naphthyl moiety of [ZnCl2L]2, gradually decreases with the addition of CH2I2. And washing off the CH2I2 by dichloromethane returned the PL intensity back to its approximately original signal.

Keywords: metallacyclodimer, suprachannel, π⋯π interaction, molecular recognition

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Authors: M. Gowri, E. K. Girija, V. Ganesh

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Background and Significance: Among the dental infections, inflammation and infection of the root canal are common among all age groups. Currently, the management of root canal infections involves cleaning the canal with powerful irrigants followed by intracanal medicament application. Though these treatments have been in vogue for a long time, root canal failures do occur. Treatment for root canal infections is limited due to the anatomical complexity in terms of small micrometer volumes and poor penetration of drugs. Thus, infections of the root canal seem to be a challenge that demands development of new agents that can eradicate C. albicans. Methodology: In the present study, we synthesized and screened silver-curcumin nanoparticle against Candida albicans. Detailed molecular studies were carried out with silver-curcumin nanoparticle on C. albicans pathogenicity. Morphological cell damage and antibiofilm activity of silver-curcumin nanoparticle on C. albicans was studied using scanning electron microscopy (SEM). Biochemical evidence for membrane damage was studied using flow cytometry. Further, the antifungal activity of silver-curcumin nanoparticle was evaluated in an ex vivo dentinal tubule infection model. Results: Screening data showed that silver-curcumin nanoparticle was active against C. albicans. Silver-curcumin nanoparticle exerted time kill effect and post antifungal effect. When used in combination with fluconazole or nystatin, silver-curcumin nanoparticle revealed a minimum inhibitory concentration (MIC) decrease for both drugs used. In-depth molecular studies with silver-curcumin nanoparticle on C. albicans showed that silver-curcumin nanoparticle inhibited yeast to hyphae (Y-H) conversion. Further, SEM images of C. albicans showed that silver-curcumin nanoparticle caused membrane damage and inhibited biofilm formation. Biochemical evidence for membrane damage was confirmed by increased propidium iodide (PI) uptake in flow cytometry. Further, the antifungal activity of silver-curcumin nanoparticle was evaluated in an ex vivo dentinal tubule infection model, which mimics human tooth root canal infection. Confocal laser scanning microscopy studies showed eradication of C. albicans and reduction in colony forming unit (CFU) after 24 h treatment in the infected tooth samples in this model. Conclusion: The results of this study can pave the way for developing new antifungal agents with well deciphered mechanisms of action and can be a promising antifungal agent or medicament against root canal infection.

Keywords: C. albicans, ex vivo dentine model, inhibition of biofilm formation, root canal infection, yeast to hyphae conversion inhibition

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Authors: Amir Razmjou, Elika Karbassi Yazdi

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Several direct lithium extraction (DLE) technologies have been developed for Li extraction from different brines. Although laboratory studies showed that they can technically recover Li to 90%, challenges still remain in developing a sustainable process that can serve as a foundation for the lithium dependent low-carbon economy. There is a continuing quest for DLE technologies that do not need extensive pre-treatments, fewer materials, and have simplified extraction processes with high Li selectivity. Here, an overview of DLE technologies will be provided with an emphasis on the basic principles of the materials’ design for the development of membranes with nanochannels and nanopores with Li ion selectivity. We have used a variety of building blocks such as nano-clay, organic frameworks, Graphene/oxide, MXene, etc., to fabricate the membranes. Molecular dynamic simulation (MD) and density functional theory (DFT) were used to reveal new mechanisms by which high Li selectivity was obtained.

Keywords: lithium recovery, membrane, lithium selectivity, decarbonization

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Authors: Alejandro Villegas, Cihan Varol

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Voice over Internet Protocol (VoIP) products is an emerging technology that can contain forensically important information for a criminal activity. Without having the user name and passwords, this forensically important information can still be gathered by the investigators. Although there are a few VoIP forensic investigative applications available in the literature, most of them are particularly designed to collect evidence from the Skype product. Therefore, in order to assist law enforcement with collecting forensically important information from variety of Betamax VoIP tools, CVOIP-FRU framework is developed. CVOIP-FRU provides a data gathering solution that retrieves usernames, contact lists, as well as call and SMS logs from Betamax VoIP products. It is a scripting utility that searches for data within the registry, logs and the user roaming profiles in Windows and Mac OSX operating systems. Subsequently, it parses the output into readable text and html formats. One superior way of CVOIP-FRU compared to the other applications that due to intelligent data filtering capabilities and cross platform scripting back end of CVOIP-FRU, it is expandable to include other VoIP solutions as well. Overall, this paper reveals the exploratory analysis performed in order to find the key data paths and locations, the development stages of the framework, and the empirical testing and quality assurance of CVOIP-FRU.

Keywords: betamax, digital forensics, report utility, VoIP, VoIPBuster, VoIPWise

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Authors: Krutika K. Sawant, Anil Solanki

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The present study deals with the preparation and optimization of ethyl cellulose-containing disopyramide phosphate loaded microspheres using solvent evaporation technique. A central composite design consisting of a two-level full factorial design superimposed on a star design was employed for optimizing the preparation microspheres. The drug:polymer ratio (X1) and speed of the stirrer (X2) were chosen as the independent variables. The cumulative release of the drug at a different time (2, 6, 10, 14, and 18 hr) was selected as the dependent variable. An optimum polynomial equation was generated for the prediction of the response variable at time 10 hr. Based on the results of multiple linear regression analysis and F statistics, it was concluded that sustained action can be obtained when X1 and X2 are kept at high levels. The X1X2 interaction was found to be statistically significant. The drug release pattern fitted the Higuchi model well. The data of a selected batch were subjected to an optimization study using Box-Behnken design, and an optimal formulation was fabricated. Good agreement was observed between the predicted and the observed dissolution profiles of the optimal formulation.

Keywords: disopyramide phosphate, ethyl cellulose, microspheres, controlled release, Box-Behnken design, factorial design

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Authors: Ioan Corneliu Salisteanu, Valentin Dogaru Ulieru, Mihaita Nicolae Ardeleanu, Alin Pohoata, Bogdan Salisteanu, Stefan Broscareanu

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Creating a personalized statistic for an individual within the population using IT systems, based on the searches and intercepted spheres of interest they manifest, is just one 'atom' of the artificial intelligence analysis network. However, having the ability to generate statistics based on individual data intercepted from large demographic areas leads to reasoning like that issued by a human mind with global strategic ambitions. The DiaMOTO device is a technical sensory system that allows the interception of car events caused by a driver, positioning them in time and space. The device's connection to the vehicle allows the creation of a source of data whose analysis can create psychological, behavioural profiles of the drivers involved. The SiaMOTO system collects data from many vehicles equipped with DiaMOTO, driven by many different drivers with a unique fingerprint in their approach to driving. In this paper, we aimed to explain the software infrastructure of the SiaMOTO system, a system designed to monitor and improve driver driving behaviour, as well as the criteria and algorithms underlying the intelligent analysis process.

Keywords: artificial intelligence, data processing, driver behaviour, driver monitoring, SiaMOTO

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Authors: Kerekoppa Puttaiah Bhatta Ramesha, Uday Kannegundla, Praseeda Mol, Lathika Gopalakrishnan, Jagish Kour Reen, Gourav Dey, Manish Kumar, Sakthivel Jeyakumar, Arumugam Kumaresan, Kiran Kumar M., Thottethodi Subrahmanya Keshava Prasad

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Spermatozoa are the highly specialized transcriptionally and translationally inactive haploid male gamete. The understanding of proteome of sperm is indispensable to explore the mechanism of sperm motility and fertility. Though there is a large number of human sperm proteomic studies, in-depth proteomic information on Bos indicus spermatozoa is not well established yet. Therefore, we illustrated the profile of sperm proteome in indigenous cattle, Malnad gidda (Bos Indicus), using high-resolution mass spectrometry. In the current study, two semen ejaculates from 3 breeding bulls were collected employing the artificial vaginal method. Using 45% percoll purification, spermatozoa cells were isolated. Protein was extracted using lysis buffer containing 2% Sodium Dodecyl Sulphate (SDS) and protein concentration was estimated. Fifty micrograms of protein from each individual were pooled for further downstream processing. Pooled sample was fractionated using SDS-Poly Acrylamide Gel Electrophoresis, which is followed by in-gel digestion. The peptides were subjected to C18 Stage Tip clean-up and analyzed in Orbitrap Fusion Tribrid mass spectrometer interfaced with Proxeon Easy-nano LC II system (Thermo Scientific, Bremen, Germany). We identified a total of 6773 peptides with 28426 peptide spectral matches, which belonged to 1081 proteins. Gene ontology analysis has been carried out to determine the biological processes, molecular functions and cellular components associated with sperm protein. The biological process chiefly represented our data is an oxidation-reduction process (5%), spermatogenesis (2.5%) and spermatid development (1.4%). The highlighted molecular functions are ATP, and GTP binding (14%) and the prominent cellular components most observed in our data were nuclear membrane (1.5%), acrosomal vesicle (1.4%), and motile cilium (1.3%). Seventeen percent of sperm proteins identified in this study were involved in metabolic pathways. To the best of our knowledge, this data represents the first total sperm proteome from indigenous cattle, Malnad Gidda. We believe that our preliminary findings could provide a strong base for the future understanding of bovine sperm proteomics.

Keywords: Bos indicus, Malnad Gidda, mass spectrometry, spermatozoa

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Authors: B. M. Patil

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Calcium Zirconate (CaZrO3) has high protonic conductivities at elevated temperature in water or hydrogen atmosphere. Undoped calcium zirconate acts as a p-type semiconductor in air. In this paper, we reported synthesis of CaZrO3 nanoparticles via modified molecular precursor method. The precursor calcium zirconium oxalate (CZO) was synthesized by exchange reaction between freshly generated aqueous solution of sodium zirconyl oxalate and calcium acetate at room temperature. The controlled pyrolysis of CZO in air at 700°C for one hour resulted in the formation nanocrystalline CaZrO3 powder. CaZrO3 obtained by the present method was characterized by Simultaneous thermogravimetry and differential thermogravimetry (TG-DTA), X-ray diffraction (XRD), infra-red spectroscopy and transmission electron microscopy (TEM). The pellets of synthesized CaZrO3 fabricated, sintered at 1000°C for 5 hr and tested as sensors for NO2 and NH3 gases.

Keywords: CaZrO3, CZO, NO2, NH3

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Authors: Mads H. Clausen

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Plant cell walls are structurally complex and contain a larger number of diverse carbohydrate polymers. These plant fibers are a highly valuable bio-resource and the focus of food, energy and health research. We are interested in studying the interplay of plant cell wall carbohydrates with proteins such as enzymes, cell surface lectins and antibodies. However, detailed molecular level investigations of such interactions are hampered by the heterogeneity and diversity of the polymers of interest. To circumvent this, we target well-defined oligosaccharides with representative structures that can be used for characterizing protein-carbohydrate binding. The presentation will highlight chemical syntheses of plant cell wall oligosaccharides from our group and provide examples from studies of their interactions with proteins.

Keywords: oligosaccharides, carbohydrate chemistry, plant cell walls, carbohydrate-acting enzymes

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Authors: Kashif Hassan, M.A. Ahanger

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Floods have become more frequent and severe due to effects of global climate change and human alterations of the natural environment. Flood prediction/ forecasting and control is one of the greatest challenges facing the world today. The forecast of floods is achieved by the use of hydraulic models such as HEC-RAS, which are designed to simulate flow processes of the surface water. Extreme flood events in river Jhelum , lasting from a day to few are a major disaster in the State of Jammu and Kashmir, India. In the present study HEC-RAS model was applied to two different reaches of river Jhelum in order to estimate the flood levels corresponding to 25, 50 and 100 year return period flood events at important locations and to deduce flood vulnerability of important areas and structures. The flow rates for the two reaches were derived from flood-frequency analysis of 50 years of historic peak flow data. Manning's roughness coefficient n was selected using detailed analysis. Rating Curves were also generated to serve as base for determining the boundary conditions. Calibration and Validation procedures were applied in order to ensure the reliability of the model. Sensitivity analysis was also performed in order to ensure the accuracy of Manning's n in generating water surface profiles.

Keywords: flood plain, HEC-RAS, Jhelum, return period

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Authors: Wen Po Cheng, Chia Yun Chung, Ruey Fang Yu, Chao Feng Chen

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The main objective of this research was to study the differences of aluminum hydrolytic products between two PACl preparation methods. These two methods were the acidification process of freshly formed amorphous Al(OH)₃ and the conventional alkalization process of aluminum chloride solution. According to Ferron test and ²⁷Al NMR analysis of those two PACl preparation procedures, the reaction rate constant (k) values and Al₁₃ percentage of acid addition process at high basicity value were both lower than those values of the alkaline addition process. The results showed that the molecular structure and size distribution of the aluminum species in both preparing methods were suspected to be significantly different at high basicity value.

Keywords: polyaluminum chloride, Al13, amorphous aluminum hydroxide, Ferron test

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Authors: Mehdi Tavana, Seyedeh Zeinab Peighambarzadeh

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Pyelography is used for morphologic and especially functional studies of the urinary tracts. There are many indications for excretory Pyelography in humans and animals. Intravenous Pyelography is the most practical method; other Pyelography techniques were manipulated because of difficulties for finding veins in small size of the patients. At the best of times, the combination of small veins and abundant subcutaneous tissue makes vascular access difficult or impossible, therefore, another methods of administration of contrast media is desired. This study was performed to evaluate the feasibility of intraosseous injection of iodixanol in providing a safe and diagnostic urogram in Persian squirrel. Fourteen hundred mg iodine per kilogram body weight of iodixanol was injected subcutaneously over tibial tuberosity on ten clinically healthy adult Persian squirrels with no signs of urinary system disorder. Lateral and ventrodorsal radiographs were taken every 2 minutes until the pyelogram was finished. Intraosseous injection of iodixanol was successful to show nephrogram, pyelogram, uretrogram and cystogram clearly. There were no abnormal clinical signs after one week of experiments. Biochemical and hematological profiles were in normal ranges. It is concluded that intraosseous Pyelography is an effective and reliable method for Pyelography studies in squirrel. Microscopic examinations of the kidneys and the site of injection after one week were normal.

Keywords: pyelography, intraosseous injection, iodixanol, persian squirrel

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Authors: Amani Tahat, Serdal Kirmizialtin

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Trajectory fragment methods such as Markov State Models (MSM), Milestoning (MS) and Transition Path sampling are the prime choice of extending the timescale of all atom Molecular Dynamics simulations. In these approaches, a set of structures that covers the accessible phase space has to be chosen a priori using cluster analysis. Structural clustering serves to partition the conformational state into natural subgroups based on their similarity, an essential statistical methodology that is used for analyzing numerous sets of empirical data produced by Molecular Dynamics (MD) simulations. Local transition kernel among these clusters later used to connect the metastable states using a Markovian kinetic model in MSM and a non-Markovian model in MS. The choice of clustering approach in constructing such kernel is crucial since the high dimensionality of the biomolecular structures might easily confuse the identification of clusters when using the traditional hierarchical clustering methodology. Of particular interest, in the case of MS where the milestones are very close to each other, accurate determination of the milestone identity of the trajectory becomes a challenging issue. Throughout this work we present two cluster analysis methods applied to the cis–trans isomerism of dinucleotide AA. The choice of nucleic acids to commonly used proteins to study the cluster analysis is two fold: i) the energy landscape is rugged; hence transitions are more complex, enabling a more realistic model to study conformational transitions, ii) Nucleic acids conformational space is high dimensional. A diverse set of internal coordinates is necessary to describe the metastable states in nucleic acids, posing a challenge in studying the conformational transitions. Herein, we need improved clustering methods that accurately identify the AA structure in its metastable states in a robust way for a wide range of confused data conditions. The single linkage approach of the hierarchical clustering available in GROMACS MD-package is the first clustering methodology applied to our data. Self Organizing Map (SOM) neural network, that also known as a Kohonen network, is the second data clustering methodology. The performance comparison of the neural network as well as hierarchical clustering method is studied by means of computing the mean first passage times for the cis-trans conformational rates. Our hope is that this study provides insight into the complexities and need in determining the appropriate clustering algorithm for kinetic analysis. Our results can improve the effectiveness of decisions based on clustering confused empirical data in studying conformational transitions in biomolecules.

Keywords: milestoning, self organizing map, single linkage, structure clustering

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Authors: Sabah El-Sawalhi, Elie Fayad, Roula M. Abdel-Massih

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Ilex paraguariensis (Yerba Mate) is a medium to large tree commonly consumed by South Americans. Its leaves and stems are associated with different biological activities. The purpose of this study was to evaluate the antibacterial activity of Yerba Mate against Gram-positive and Gram-negative bacterial strains and its action against some resistant bacteria with different resistance profiles. Yerba Mate aqueous extracts were prepared at 70°C for 2 hrs, and the microdilution method was used to determine the minimum inhibitory concentration (MIC). Gram-positive bacteria exhibited a stronger antibacterial activity (MIC ranged between 0.468 mg/mL and 15 mg/mL) than Gram-negative bacteria. Yerba Mate was also extracted with acetone: water (1:1) and then further sub-fractionated with hexane, chloroform, and ethyl acetate. MIC values against Staphylococcus aureus ranged from 0.78 to 2.5 mg/ml for the chloroform fraction, from 1.56 to 3.75 mg/ml for the ethyl acetate fraction, and 0.78 to 1.87 mg/ml for the water fraction. The water fraction also exhibited antibacterial activity against Salmonella species (MIC ranged from 1.56 mg/ml to 3.12 mg/ml). The water fraction exhibited the highest antibacterial activity among all the fractions obtained. More studies are needed to determine the molecule or molecules responsible for this activity.

Keywords: antibacterial activity, bacterial resistance, minimum inhibitory concentration, yerba mate

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Authors: Afaf Benhouda, Mouloud Yahia, Hachani Khadraoui, Asma Meddour, Souhila Benbia, Abdelmoudjib Ghecham, Djahida Benhouda

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Umbilicus rupestris (UR) is an herbal medicine traditionally applied against the ignitions of the skin. The present paper aimed to study the acute and subacute toxicity with orally administered methanolic leaves extract of Umbilicus rupestris L (URMeOH). In acute toxicity tests, four groups of rats (n = 6/group/female) were orally treated with doses of 500, 1000, 1500 and 2000 mg/kg, and general behaviour, adverse effects, and mortality were recorded for up to 14 days. In subacute toxicity study, rats received URAMeOH by gavage at the doses of 100, 200 mg/kg/day (n = 6/group) for 28 days, and biochemical, hematological, and histopathological changes in tissues (liver, kidney) were determined. URMeOH did not produce any hazardous symptoms or death and in the acute toxicity test. Subacute treatment with URMeOH did not show any change in body weight, and hematological and biochemical profiles. In addition, no change was observed either in macroscopic or microscopic aspects of vital organs in rats. Our result showed that Umbilicus rupestris extract could be safe for human use.

Keywords: acute toxicity, biochemical parameters, hematological parameters, Umbilicus rupestris, subacute toxicity

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Authors: A. Dali-Ali, F. Agag, H. Beldjilali, A. Oukebdane, K. Meddeber, R. Dali-Yahia, N. Midoun

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The ability of Acinetobacter baumannii to develop multiple resistances towards to the majority of antibiotics explains the therapeutic difficulties encountered in severe infections. Furthermore, its persistence in the humid or dry environment promotes cross-contamination in intensive care units. The aim of our study was to describe the epidemiological and bacterial resistance profiles of hospital-acquired infections caused by Acinetobacter baumannii in the intensive care unit of our teaching hospital. During the study period (June 3, 2012 to December 31, 2013), 305 patients having duration of hospitalization equal or more than 48 hours were included in the study. Among these, 36 had developed, at least, one health-care associated infection caused by Acinetobacter baumannii. The rate of infected patients was equal to 11.8% (36/305). The rate of cumulative incidence of hospital-acquired pneumonia was the highest (9.2%) followed by central venous catheter infection (1.3%). Analysis of the various antibiotic resistance profile shows that 93.8% of the strains were resistant to imipenem. The nosocomial infection control committee set up a special program not only to reduce the high rates of incidence of these infections but also to descrease the rate of imipenem resistance.

Keywords: Acinetobacer baumannii, epidemiological profile, hospital acquired infections, intensive care unit

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Authors: B. Roopa Sri, Y Lakshmi Naidu

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Chemical Graph Theory (CGT) is the branch of mathematical chemistry in which molecules are modeled to study their physicochemical properties using molecular descriptors. Amongst these descriptors, topological indices play a vital role in predicting the properties by defining the graph topology of the molecule. Recently, the bond-additive topological index known as the Mostar index has been proposed. In this paper, we compute the Mostar-type indices of octane isomers and use the data obtained to perform QSPR analysis. Furthermore, we show the correlation between the Mostar type indices and the properties.

Keywords: chemical graph theory, mostar type indices, octane isomers, qspr analysis, topological index

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Authors: Valeria Velasco, Ana M. Bonilla, José L. Vergara, Alcides Lofa, Jorge Campos, Pedro Rojas-García

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Staphylococcus aureus is both commensal bacterium and opportunistic pathogen that can cause different diseases in humans and can rapidly develop antimicrobial resistance. Since this bacterium has the ability to colonize the nares and skin of humans and animals, there is a risk of contamination of food in different steps of the food chain supply. Emerging strains have been detected in food-producing animals and meat, such as methicillin-resistant S. aureus (MRSA). The aim of this study was to determine the prevalence and oxacillin susceptibility of S. aureus in the pork chain supply in Chile and to suggest some natural antimicrobials for control. A total of 487 samples were collected from pigs (n=332), carcasses (n=85), and retail pork meat (n=70). Presumptive S. aureus colonies were isolated by selective enrichment and culture media. The confirmation was carried out by biochemical testing (Api® Staph) and molecular technique PCR (detection of nuc and mecA genes, associated with S. aureus and methicillin resistance, respectively). The oxacillin (β-lactam antibiotic that replaced methicillin) susceptibility was assessed by minimum inhibitory concentration (MIC) using the Epsilometer test (Etest). A preliminary assay was carried out to test thymol, carvacrol, oregano essential oil (Origanum vulgare L.), Maqui or Chilean wineberry extract (Aristotelia chilensis (Mol.) Stuntz) as anti-staphylococcal agents using the disc diffusion method at different concentrations. The overall prevalence of S. aureus in the pork chain supply reached 33.9%. A higher prevalence of S. aureus was determined in carcasses (56.5%) than in pigs (28.3%) and pork meat (32.9%) (P ≤ 0.05). The prevalence of S. aureus in pigs sampled at farms (40.6%) was higher than in pigs sampled at slaughterhouses (23.3%) (P ≤ 0.05). The contamination of no packaged meat with S. aureus (43.1%) was higher than in packaged meat (5.3%) (P ≤ 0.05). The mecA gene was not detected in S. aureus strains isolated in this study. Two S. aureus strains exhibited oxacillin resistance (MIC ≥ 4µg/mL). Anti-staphylococcal activity was detected in solutions of thymol, carvacrol, and oregano essential oil at all concentrations tested. No anti-staphylococcal activity was detected in Maqui extract. Finally, S. aureus is present in the pork chain supply in Chile. Although the mecA gene was not detected, oxacillin resistance was found in S. aureus and could be attributed to another resistance mechanism. Thymol, carvacrol, and oregano essential oil could be used as anti-staphylococcal agents at low concentrations. Research project Fondecyt No. 11140379.

Keywords: antimicrobials, mecA gen, nuc gen, oxacillin susceptibility, pork meat

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Authors: N. Hachemi, A. Nouani, A. Benchabane

Abstract:

The influence of cultivation factors such as content of ammonium sulfate, glucose and water in the culture medium and particle size of dry orange waste, on their bioconversion for pectinase production was studied using complete factorial design. a polygalacturonase (PG) was isolated using ion exchange chromatography under gradient elution 0-0,5 m/l NaCl (column equilibrate with acetate buffer pH 4,5), subsequently by sephadex G75 column chromatography was applied and the molecular weight was obtained about 51,28 KDa . Purified PG enzyme exhibits a pH and temperature optima of activity at 5 and 35°C respectively. Treatment of apple juice by purified enzyme extract yielded a clear juice, which was competitive with juice yielded by pure Sigma Aldrich Aspergillus niger enzyme.

Keywords: bioconversion, orange wastes, optimization, pectinase

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Authors: Yosra M. Badiei, Evelyn Ortiz, Marisa Portenti, David Szalda

Abstract:

Water-oxidation half-reaction is a critical reaction that can be driven by a sustainable energy source (e.g., solar or wind) and be coupled with a chemical fuel making reaction which stores the released electrons and protons from water (e.g., H₂ or methanol). The use of molecular water-oxidation catalysts (WOC) allow the rationale design of redox active metal centers and provides a better understanding of their structure-activity-relationship. Herein, the structure of a Ru(III) complex bearing a doubly deprotonated N,N'-bis(aryl)pyridine-2,6-dicarboxamide ligand which contains a water molecule in its primary coordination sphere was elucidated by single-crystal X-ray diffraction. Further spectroscopic experimental data and pH-dependent electrochemical studies reveal its water-oxidation reactivity. Emphasis on mechanistic details for O₂ formation of this complex will be addressed.

Keywords: water-oxidation, catalysis, ruthenium, artificial photosynthesis

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Authors: Makito Sakai, Takahiro Kiwata, Takumi Awa, Hiroshi Teramoto, Takaaki Kono, Kuniaki Toyoda

Abstract:

Using experimental and numerical results, this paper describes the effects of tabs on the flow characteristics of a plane jet at comparatively low Reynolds numbers while focusing on the velocity field and the vortical structure. The flow visualization and velocity measurements were respectively carried out using laser Doppler velocimetry (LDV) and particle image velocimetry (PIV). In addition, three-dimensional (3D) plane jet numerical simulations were performed using ANSYS Fluent, a commercially available computational fluid dynamics (CFD) software application. We found that the spreads of jets perturbed by large delta tabs and round tabs were larger than those produced by the other tabs tested. Additionally, it was determined that a plane jet with square tabs had the smallest jet spread downstream, and the jet’s centerline velocity was larger than those of jets perturbed by the other tabs tested. It was also observed that the spanwise vortical structure of a plane jet with tabs disappeared completely. Good agreement was found between the experimental and numerical simulation velocity profiles in the area near the nozzle exit when the laminar flow model was used. However, we also found that large eddy simulation (LES) is better at predicting the developing flow field of a plane jet than the laminar and the standard k-ε turbulent models.

Keywords: plane jet, flow control, tab, flow measurement, numerical simulation

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Authors: Mehdi Ghatei, Masoomeh Lorestani

Abstract:

Upstream Tailings Storage Facilities (TSFs) may experience slope instabilities due to soil liquefaction, especially in regions known to be seismically active. In this study, liquefaction susceptibility of an upstream-raised TSF in Western Australia was assessed using two different approaches. The first approach assessed liquefaction susceptibility using Cone Penetration Tests with pore pressure measurement (CPTu) as described by the National Centre for Earthquake Engineering Research (NCEER). This assessment was based on the four CPTu tests that were conducted on the perimeter embankment of the TSF. The second approach used the Finite Element (FE) method with application of an equivalent linear model to predict the undrained cyclic behavior, the pore water pressure and the liquefaction of the materials. The tailings parameters were estimated from the CPTu profiles and from the laboratory tests. The cyclic parameters were estimated from the literature where test results of similar material were available. The results showed that there was a good agreement, in the liquefaction susceptibility of the tailings material, between the NCEER and FE methods with equivalent linear model.

Keywords: liquefaction , CPTU, NCEER, finite element method, equivalent linear model

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Authors: Caroline Mendes, Mary McNamara, Orla Howe

Abstract:

For chemotherapy, a drug delivery system should be able to specifically target cancer cells and deliver the therapeutic dose without affecting normal cells. Folate receptors (FR) can be considered key targets since they are commonly over-expressed in cancer cells and they are the molecular marker used in this study. Here, cyclodextrin (CD) has being studied as a vehicle for delivering the chemotherapeutic drug, methotrexate (MTX). CDs have the ability to form inclusion complexes, in which molecules of suitable dimensions are included within the CD cavity. In this study, β-CD has been modified using folic acid so as to specifically target the FR molecular marker. Thus, the system studied here for drug delivery consists of β-CD, folic acid and MTX (CDEnFA:MTX). Cellular uptake of folic acid is mediated with high affinity by folate receptors while the cellular uptake of antifolates, such as MTX, is mediated with high affinity by the reduced folate carriers (RFCs). This study addresses the gene (mRNA) and protein expression levels of FRs and RFCs in the cancer cell lines CaCo-2, SKOV-3, HeLa, MCF-7, A549 and the normal cell line BEAS-2B, quantified by real-time polymerase chain reaction (real-time PCR) and flow cytometry, respectively. From that, four cell lines with different levels of FRs, were chosen for cytotoxicity assays of MTX and CDEnFA:MTX using the MTT assay. Real-time PCR and flow cytometry data demonstrated that all cell lines ubiquitously express moderate levels of RFC. These experiments have also shown that levels of FR protein in CaCo-2 cells are high, while levels in SKOV-3, HeLa and MCF-7 cells are moderate. A549 and BEAS-2B cells express low levels of FR protein. FRs are highly expressed in all the cancer cell lines analysed when compared to the normal cell line BEAS-2B. The cell lines CaCo-2, MCF-7, A549 and BEAS-2B were used in the cell viability assays. 48 hours treatment with the free drug and the complex resulted in IC50 values of 93.9 µM ± 9.2 and 56.0 µM ± 4.0 for CaCo-2 for free MTX and CDEnFA:MTX respectively, 118.2 µM ± 10.8 and 97.8 µM ± 12.3 for MCF-7, 36.4 µM ± 6.9 and 75.0 µM ± 8.5 for A549 and 132.6 µM ± 12.1 and 288.1 µM ± 16.3 for BEAS-2B. These results demonstrate that MTX is more toxic towards cell lines expressing low levels of FR, such as the BEAS-2B. More importantly, these results demonstrate that the inclusion complex CDEnFA:MTX showed greater cytotoxicity than the free drug towards the high FR expressing CaCo-2 cells, indicating that it has potential to target this receptor, enhancing the specificity and the efficiency of the drug.

Keywords: cyclodextrins, cancer treatment, drug delivery, folate receptors, reduced folate carriers

Procedia PDF Downloads 299