Search results for: molecular topology

Authors: M. Ben Jrad, A. Belhaj Mohamed, S. Riahi, I. Bouazizi, M. Saidi, M. Soussi

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The generative potential, depositional environment, thermal maturity and oil seeps of the organic-rich Bou Dabbous Formation (Ypresian) from the thrust belt northwestern Tunisia, were determined by Rock Eval and molecular analyses. The paleo-tectonic units in the area show some similarities with equivalent facies in Mediterranean Sea and Sicilian. The Bou Dabbous Formation displays variable source rock characteristics through the various units Tellian and Numidian nappes Units. Organic matter contents and petroleum potentials are fair to high (reaching 1.95% and 6 kg of HC/t of rock respectively) marine type II kerogen. An increasing SE-NW maturity gradient is well documented in the study area. The Bou Dabbous organic-rich facies are marginally mature stage in the Tellian Unit (Kasseb domain), whilst they are mature-late mature stage within Nefza-Ain Allega tectonic windows. A long and north of Cap Serrat-Ghardimaou Master Fault these facies are overmature. Oil/Oil and Oil/source rock correlation, based on biomarker and carbon isotopic composition, shows a positive genetic correlation between the oil seeps and Bou Dabbous source rock.

Keywords: biomarkers, Bou Dabbous Formation, Northern Tunisia, source rock

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Authors: Hatairuk Tungkasen, Somrudee Phetchrid, Suwapat Jaidee, Supinya Yoomak, Chantana Kankamol, Mayuree Pumipaiboon, Mayuva Areekijseree

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Ovaries of reproductive female pigs were obtained from local slaughterhouses in Nakorn Pathom Province, Thailand. Follicular fluid of medium follicle (5-6 diameters) and large follicles (7-8 mm and 10 mm in diameter) were aspirated and collected by sterile technique and analyzed protein pattern. The follicular fluid protein bands were found by SDS-PAGE which has no protein band in difference compared to standard protein band. So we chose protein band molecular weight 50, 62-65, 75-80, 90, 120-160, and >220 kDa were analyzed by LC/MS/MS. The result was found immunoglobulin gamma chain, keratin, transferrin, heat shock protein, and plasminogen precursor, ceruloplasmin, and hemopexin, and protease, respectively. All proteins play important roles in promotion and regulation on growth and development of reproductive cells. The result of this study found many proteins which were useful and important for in vitro oocyte maturation and embryonic development of cell technology in animals. The further study will be use porcine follicular fluid protein of medium and large follicles as feeder cells in in vitro condition to promote oocyte and embryo maturation.

Keywords: follicular fluid protein, LC/MS/MS, porcine oocyte, SDS-PAGE

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Authors: Pablo Vidal, Misael Martinez, Carlos Hernandez, Ananta R. Adhikari, Luis Materon, Yuanbing Mao, Karen Lozano

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Conjugated polymers are smart materials that show tremendous practical applications in diverse subjects. Polydiacetylenes are conjugated polymers with special optical properties. In response to the environmental changes such as pH and molecular binding, it changes its color. Such an interesting chromic and emissive behavior of polydiacetylenes make them a highly popular polymer in wide areas, including biomedicine such as a biosensor. In this research, we used polyvinyl butyrate as a matrix to fibrillate polydiacetylenes. We initially prepared polyvinyl butyrate/diacetylene matrix using forcespinning technique. They were then polymerized to form polyvinyl butyrate/polydiacetylene (PVB/PDA). These matrices then studied for their bio-sensing response to gram-positive and gram-negative bacteria. The sensing ability of the PVB/PDA biosensor was observed as early as 30 min in the presence of bacteria at 37°C. Now our effort is to decrease this effective temperature to room temperature to make this device applicable in the general daily life. These chromic biosensors will find extensive application not only alert the infection but also find other promising applications such as wearable sensors and diagnostic systems.

Keywords: smart material, conjugated polymers, biosensor, polyvinyl butyrate/polydiacetylene

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Authors: Moshe Mello, Hilary Rutto, Tumisang Seodigeng

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The accelerating requirement to reach 0% sulfur content in liquid fuels demands researchers to seek efficient alternative technologies to challenge the predicament. In this current study, the adsorption capabilities of modified Cu(I)-Y zeolite were tested for removal of organosulfur compounds (OSC) present in TPO. The π-complexation-based adsorbent was obtained by ion exchanging Y-zeolite with Cu+ cation using liquid phase ion exchange (LPIE). Preparation of the adsorbent involved firstly ion-exchange between Na-Y zeolite with a Cu(NO3)2 aqueous solution of 0.5M for 48 hours followed by reduction of Cu2+ to Cu+. Batch studies for TPO in comparison with model diesel comprising of sulfur compounds such as thiophene (TH), benzothiophene (BTH), dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophe (4,6-DMDBT) showed that modified Cu(I)-Y zeolite is an effective adsorbent for removal of OSC in liquid fuels. The effect of multiple operating conditions such as adsorbent dosage, reaction time and temperature were studied to optimize the process. For model diesel fuel, the selectivity for adsorption of sulfur compounds followed the order 4,6-DMDBT> DBT> BTH> TH. Interpretation of the results was justified using the molecular orbital theory and calculations. Langmuir and Freundlich isotherms were used to predict adsorption of the reaction mixture. The Cu(I)-Y zeolite is fully regeneratable and this is achieved by a simple procedure of blowing the adsorbent with air at 350 °C, followed by reactivation at 450 °C in a rich helium surrounding.

Keywords: adsorption, desulfurization, TPO, zeolite

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Authors: Hamid Hossein Khezri, Afsaneh Javdani-Mallak

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Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Cannabidiol (CBD) is one of the members of cannabinoid compounds found in cannabis. CBD and Cannabinol (CBN), as the other extract of plant Cannabis, were able to reduce myofascial pain in rats with immunosuppressive and anti-inflammatory activities. In this study, we accomplished protein-protein BLAST and the sequence was found to be for Gamma-aminobutyric acid receptor subunit alpha-1 (GBRA1) chain A and its 3D structure was subsequently downloaded from Protein Data Bank. The structures of the ligands cannabinol and cannabidiol were obtained from PubChem. After a necessary process of the obtained files, AutoDock Vina was used to performing molecular docking. Docking between the ligands and GBRA1 chain A revealed that cannabinol has a higher affinity to GBRA1 (binding energy = -7.5 kcal/mol) compared to cannabidiol (binding energy = -6.5 kcal/mol). Furthermore, cannabinol seems to be able to interact with 10 residues of the protein, out of which 3 are in the neurotransmitter-gated ion-channel transmembrane domain of GBRA1, whereas cannabidiol interacts with two other residues. Although the results of this project do not indicate the activating /or inhibitory capability of the studied compounds, it suggests that cannabinol can act as a relatively strong ligand for GBRA1.

Keywords: protein-ligand docking, cannabinol, cannabidiol, GBRA1

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Authors: Abdelaziz Messis, Azzeddine Bettache, Nawel Boucherba, Said Benallaoua, Mouloud Kecha

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Actinobacteria are of special biotechnological interest since they are known to produce chemically diverse compounds with a wide range of biological activity. This distinct clade of Gram-positve bacteria include some of the key antibiotic producers and are also sources of several bioactive compounds, established commercially a newly filamentous bacteria was recovered from Tikjda forest soil (Algeria) for its high antifungal activity against various pathogenic and phytopathogenic fungi. The nucleotide sequence of the 16S rRNA gene (1454 pb) of Streptomyces sp. TKJ2 exhibited close similarity (99 %) with other Streptomyces16S rRNA genes. Antifungal metabolite production of Streptomyces sp TKJ2 was evaluated using six different fermentation media. The extracellular products contained potent antifungal agents. Antifungal protein produced by Streptomyces sp. TKJ2 on PCA medium has been purified by ammonium sulfate precipitation, SPE column chromatography and high-performance liquid chromatography in a reverse-phase column. The UV chromatograms of the active fractions obtained at 214 nm by NanoLC-ESI-MS/MS have different molecular weights. The F20 Peptidic fraction obtained from culture filtrat of Streptomyces sp. TKJ2 precipitated at 30% of ammonium sulfate was selected for analysis by infusion ESI-MS which yielded a singly charged ion mass of 437.17 Da.

Keywords: actinobacteria, antifungal protein, chromatography, Streptomyces

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Authors: Yaxin Tang, Mingao Hou, Qian He, Guangfu Luo

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Bimetallic nanoparticles serve as a promising class of catalysts with tunable properties suitable for diverse catalytic reactions, yet a comprehensive understanding of their actual structures under operating conditions and the optimal design principles remains largely elusive. In this study, we unveil a prevalent surface segregation phenomenon in nearly 100 platinum-group-element-based bimetallic nanoparticles through first principles-based molecular dynamics simulations. Our findings highlight that two components in a nanoparticle with relatively lower surface energy tend to segregate to the surface. Motivated by this discovery, we propose a deliberate exploitation of surface segregation in designing bimetallic nanoparticle catalysts, aiming for heightened stability and reduced consumption of precious metals. To validate this strategy, we further investigate 36 platinum-based bimetallic nanoparticles for propane dehydrogenation catalysis. Through a systematic examination of catalytic sites on nanoparticles, we identify several systems as top candidates with Pt-enriched surfaces, remarkable thermal stability, and superior catalytic activity for propane dehydrogenation. The insights gained garnered from this study are anticipated to provide a valuable framework for the optimal design of other bimetallic nanoparticles.

Keywords: bimetallic nanoparticles, platinum-group element, catalysis, surface segregation, first-principles calculations

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Authors: Shakir H. Mohammed Al-Alwany, Saad Hasan M. Ali, Ibrahim Mohammed S. Shnawa

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The study was aimed to define the percentage of detection of high-oncogenic risk types of HPV and their genotyping in archival tissue specimens that ranged from apparently healthy tissue to invasive breast cancer by using one of the recent versions of In Situ Hybridization(ISH) 0.2. To find out rational significance of such genotypes as well as over expressed products of mutants P53 and RB genes on the severity of underlying breast cancers. The DNA of HPV was detected in 46.5 % of tissues from breast cancers while HPV DNA in the tissues from benign breast tumours was detected in 12.5%. No HPV positive–ISH reaction was detected in healthy breast tissues of the control group. HPV DNA of genotypes (16, 18, 31 and 33) was detected in malignant group in frequency of 25.6%, 27.1%, 30.2% and 12.4%, respectively. Over expression of p53 was detected by IHC in 51.2% breast cancer cases and in 50% benign breast tumour group, while none of control group showed P53- over expression. Retinoblastoma protein was detected by IHC test in 49.7% of malignant breast tumours, 54.2% of benign breast tumours but no signal was reported in the tissues of control group. The significance prevalence of expression of mutated p53 & Rb genes as well as detection of high-oncogenic HPV genotypes in patients with breast cancer supports the hypothesis of an etiologic role for the virus in breast cancer development.

Keywords: human papilloma virus, P53, RB, breast cancer

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Authors: Shirin Jalili, Hadi Shirzad, Samaneh Nabavi, Somayeh Khanjani

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Forensic entomology is the science of study and analysis of insects evidences to aid in criminal investigation. Being aware of the distribution, biology, ecology and behavior of insects, which are founded at crime scene can provide information about when, where and how the crime has been committed. It has many application in criminal investigations. Its main use is estimation of the minimum time after death in suspicious death. The close association between insects and corpses and the use of insects in criminal investigations is the subject of forensic entomology. Because insects attack to the decomposing corpse and spawning on it from the initial stages. Forensic scientists can estimate the postmortem index by studying the insects population and the developing larval stages.In addition, toxicological and molecular studies of these insects can reveal the cause of death or even the identity of a victim. It also be used to detect drugs and poisons, and determination of incident location. Gathering robust entomological evidences is made possible for experts by recent Techniques. They can provide vital information about death, corpse movement or burial, submersion interval, time of decapitation, identification of specific sites of trauma, post-mortem artefacts on the body, use of drugs, linking a suspect to the scene of a crime, sexual molestations and the identification of suspects.

Keywords: Forensic entomology, post mortem interval, insects, larvae

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Authors: Giorgio Visentin, Inna S. Kalinina, Alexei A. Buchachenko

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In the ambit of intermolecular interactions, a combination rule is defined as a relation linking a potential parameter for the interaction of two unlike species with the same parameters for interaction pairs of like species. Some of their most exemplificative applications cover the construction of molecular dynamics force fields and dispersion-corrected density functionals. Here, an extended combination rule is proposed, relating the dipole-dipole dispersion coefficients for the interaction of like target species to the same coefficients for the interaction of the target and a set of partner species. The rule can be devised in two different ways, either by uniform discretization of the Casimir-Polder integral on a Gauss-Legendre quadrature or by relating the dynamic polarizabilities of the target and the partner species. Both methods return the same system of linear equations, which requires the knowledge of the dispersion coefficients for interaction between the partner species to be solved. The test examples show a high accuracy for dispersion coefficients (better than 1% in the pristine test for the interaction of Yb atom with rare gases and alkaline-earth metal atoms). In contrast, the rule does not ensure correct monotonic behavior of the dynamic polarizability of the target species. Acknowledgment: The work is supported by Russian Science Foundation grant # 17-13-01466.

Keywords: combination rule, dipole-dipole dispersion coefficient, Casimir-Polder integral, Gauss-Legendre quadrature

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Authors: Sara Sousa, Veronique Gomes, Nélio Veiga, Maria José Correia

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Objectives: To assess the presence or absence of Streptococcus mutans, Streptococcus gordonii and Streptococcus salivarius in the oral biofilm of children in an elementary school of Viseu, Portugal, and verify the relationship between Streptococcus gordonii and Streptococcus salivarius and the absence of dental caries. Methods: A cross-sectional study was designed with a final sample of 40 children aged 6-11 years old. Oral examination was accomplished with the identification of their oral health status and oral biofilm collection. Analysis of biological samples by molecular techniques of DNA isolation and identification of three Streptococci bacteria by Polimerase Chain Reaction (PCR) was made. Results: We identified Streptococcus salivarius and Streptococcus gordoni only in the lower interincisal region. These species were also present mainly in the first permanent non-decayed molars. On the contrary, Streptococcus mutans was found mostly in decayed first permanent molars. Conclusion: This preliminary study establishes a possible association between the absence of dental caries and the presence of Streptococcus gordonii and Streptococcus salivarius. Since these two species are described as alkali producers, it is suggested that their presence somehow confers protection against caries. These results support new dental caries prevention strategies based on oral biofilm modulation by enrichment with alkalinogenic species.

Keywords: dental caries, oral biofilm, Streptococcus gordonii, Streptococcus salivarius

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Authors: Chengcao Sun, Shujun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, Dejia Li

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Recently, the long non-coding RNA (lncRNA) NEAT1 has been identified as an oncogenic gene in multiple cancer types and elevated expression of NEAT1 was tightly linked to tumorigenesis and cancer progression. However, the molecular basis for this observation has not been characterized in progression of non-small cell lung cancer (NSCLC). In our studies, we identified NEAT1 was highly expressed in NSCLC patients and was a novel regulator of NSCLC progression. Patients whose tumors had high NEAT1 expression had a shorter overall survival than patients whose tumors had low NEAT1 expression. Further, NEAT1 significantly accelerates NSCLC cell growth and metastasis in vitro and tumor growth in vivo. Additionally, by using bioinformatics study and RNA pull down combined with luciferase reporter assays, we demonstrated that NEAT1 functioned as a competing endogenous RNA (ceRNA) for has-miR-377-3p, antagonized its functions and led to the de-repression of its endogenous targets E2F3, which was a core oncogene in promoting NSCLC progression. Taken together, these observations imply that the NEAT1 modulated the expression of E2F3 gene by acting as a competing endogenous RNA, which may build up the missing link between the regulatory miRNA network and NSCLC progression.

Keywords: long non-coding RNA NEAT1, hsa-miRNA-377-3p, E2F3, non-small cell lung cancer, tumorigenesis

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Authors: Daruliza Kernain, Shaharum Shamsuddin, See Too Wei Cun

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CTCF is a unique, highly conserved and ubiquitously expressed 11 zinc finger (ZF) transcriptional factor with multiple target sites. It is able to bind to various target sequences to perform different regulatory roles including promoter activation or repression, creating hormone-responsive gene silencing element, and functional block of enhancer-promoter interactions. The binding of CTCF to the essential binding site is through the combination of different ZF domain. On the other hand, BORIS for brother of the regulator of imprinted sites, which expressed only in the testis and certain cancer cell line is homology to CTCF 11 ZF domains. Since both transcriptional factors share the same ZF domains hence there is a possibility for both to bind to the same target sequences. In this study, the interaction of these two proteins to multi-functional Y-box DNA/RNA-binding factor, YB-1 was determined. The protein-protein interaction between CTCF/YB-1 and BORIS/YB-1 were discovered by Co-immuno-precipitation (CO-IP) technique through reciprocal experiment from RGBM total cell lysate. The results showed that both CTCF and BORIS were able to interact with YB-1 in Glioma RGBM cell line. To the best of our knowledge, this is the first findings demonstrating the ability of BORIS and YB-1 to form a complex in vivo.

Keywords: immunoprecipitation, CTCF/BORIS/YB-1, transcription factor, molecular medicine

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Authors: Eda Gök

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Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.

Keywords: non-local continuum mechanics, peridynamic theory, solid structures, tensile loading, flexural loading

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Authors: Fatma H. Galal, Alaaeddeen M. Seufi

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Due to the increasing usage of mobile phone, experiments were designed to investigate ‎the effect of acute dose exposure on the mosquito life cycle. 50 tubes (5 ml size) ‎containing 3 ml water and a first instar larva of the mosquito, Culex univittatus were put ‎between two mobile cell phones switched on talking mode for 4 continuous hours. A ‎control group of tubes (unexposed to radiation) were used. Larval and pupal durations ‎were calculated. Furthermore, adult emergence and sex ratio were observed for both ‎treated and control larvae. Results indicated that the employed dose of radiation reduced ‎total larval duration to about half the value of control. 1st, 2nd, 3rd and 4th larval ‎durations were reduced significantly by mobile radiation when compared to controls. ‎Meanwhile pupal duration was elongated significantly by mobile radiation when ‎compared to control. Sex ratio was significantly shifted in favor of females in the case of ‎radiated mosquitoes. Successful adult emergence was decreased significantly in the case ‎of radiated insects when compared to controls. Molecular studies to investigate the ‎effects of mobile radiation on insects and other model organisms are going on.‎

Keywords: mosquito, mobilr radiation, larval and pupal durations, sex ratio

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Authors: K. F. Md Yunos, N. S. Pajar, N. S. Azmi

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Oily wastewater in Malaysian refinery has become a big issue of water and environment pollution to be solved urgently. The results of an experimental study on separation of oily wastewaters are presented. The characteristic of filtration behavior of commercial polymer ultrafiltration (UF) membranes was evaluated in the treatment of oily wastewater from palm oil refinery. The performance of different molecular weight cut off 5kDa and 10kDa regenerated cellulose membrane were evaluated and compared and the fouling behavior were analyzed by scanning electron microscopy (SEM). The effect of pressure (0.5, 1.0, 1.5, 2.0, 2.5 bar) and sample concentration (100%, 75%, 50%, 25%) on fouling of 5kDa and 10kDa membrane were evaluated. The characteristic of the sample solutions were analyzed for turbidity, total dissolved solid (TDS), total suspended solid (TSS), BOD, and COD. The results showed that the best fit to experimental data corresponds to the cake layer formation followed by the intermediate blocking for the experimental conditions tested. A more detailed analysis of the fouling mechanisms was studied by dividing the filtration curves into different regions corresponding to the different fouling mechanisms. Intermediate blocking and cake layer formation or combinations of them were found to occur during the UF experiments depending on the operating conditions.

Keywords: fouling, oily wastewater, regenerated cellulose, ultrafiltration

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Authors: Jma Hannan, Prawej Ansari, Yasser H. A. Abdel-Wahab, Peter R. Flatt

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Spirulina platensis (SP, Blue-green algae) have been accepted as a supplement for the treatment of pre and post-diabetes. The present study investigated the effects of butanol fraction from ethanol extract of S. platensis on insulin release from BRIN BD11 cells, isolated mouse islets, and perfused rat pancreas, as well as glucose homeostasis in type 2 diabetic rats and their molecular pathways. In a dose-dependent manner, S. platensis increased insulin release from mouse islets and pancreatic β-cells. The extract also elevated insulin release in perfused rat pancreas. Glucose, isobutylmethylxanthine, tolbutamide, and a depolarizing concentration of KCl significantly potentiated insulin release from BRIN BD11 cells. The effect of diazoxide and verapamil, as well as the absence of extracellular Ca2+ showed a reduction in insulin secretion. When administered orally together with glucose (2.5g/kg bw), S. platensis extract improved fasting and postprandial blood glucose in type 2 diabetes. These data suggest that the anti-diabetic activity of S. platensis is partly mediated by insulin secretion via the KATP channel-dependent pathway/the intracellular cAMP pathway.

Keywords: Insulin, glucose, S. platensis, type 2 diabetes, medicinal plants

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Authors: Ghazi Faisal Najmuldeen, Ali Abdul Rahman–Al Ezzi, Tharmathas A/L Alagappan

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The aim of this investigation was to produce biofuel from castor oil through microwave assisted thermal cracking with zeolite ZSM-5 as catalyst. The obtained results showed that microwave assisted thermal cracking of castor oil with Zeolite ZSM-5 as catalyst generates products consisting of alcohol, methyl esters and fatty acids. The products obtained from this experimental procedure by the cracking of castor oil are components of biodiesel. Samples of cracked castor oil containing 1, 3 and 5wt % catalyst was analyzed, however, only the sample containing the 5wt % catalyst showed significant presence of condensate. FTIR and GCMS studies show that the condensate obtained is an unsaturated fatty acid, is 9, 12-octadecadienoic acid, suitable for biofuel use. 9, 12-octadecadienoic acid is an unsaturated fatty acid with a molecular weight of 280.445 g/mol. Characterization of the sample demonstrates that functional group for the products from the three samples display a similar peak in the FTIR graph analysis at 1700 cm-1 and 3600 cm-1. The result obtained from GCMS shows that there are 16 peaks obtained from the sample. The compound with the highest peak area is 9, 12-octadecadienoic acid with a retention time of 9.941 and 24.65 peak areas. All these compounds are organic material and can be characterized as biofuel and biodiesel.

Keywords: castor oil, biofuel, biodiesel, thermal cracking, microwave

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Authors: K.L. Chiu, Johnny K. W. Ho, M. H. Chan, S. H. Cheung, K. H. Chan, S.K. So

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Thermal diffusivity is an important quantity in heat conduction. It measures the rate of heat transfer from the hot side to the cold side of a material. In solid-state materials, thermal diffusivity reveals information related to morphologies and solid quality, as thermal diffusivity can be affected by microstructures. However, thermal diffusivity studies on organic semiconductors are very limited. In this study, scanning photothermal deflection (SPD) technique is used to study the thermal diffusivities of different classes of semiconducting polymers. The reliability of the technique was confirmed by crossing-checking our SPD derived experimental values of different reference materials with their known diffusivities from the literature. To show that thermal diffusivity determination is a potential tool for revealing microscopic properties of organic photovoltaic semiconductors, SPD measurements were applied to various organic semiconducting films with different crystallinities. It is observed that organic photovoltaic semiconductors possess low thermal diffusivity, with values in the range of 0.3mm²/s to 1mm²/s. It is also discovered that polymeric photovoltaic semiconductors with greater molecular planarity, stronger stacking and higher crystallinity would possess greater thermal diffusivities. Correlations between thermal, charge transport properties will be discussed.

Keywords: polymer crystallinity, photovoltaic organic semiconductors, photothermal deflection technique, thermal diffusion

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Authors: Sonam Kumari

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Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, possesses a remarkable feature of entering into and emerging from a persistent state. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes.Mtb has seven such proteins (WhiB1 to WhiB7).WhiB proteins are transcriptional regulators; their conserved C-terminal HTH motif is involved in DNA binding. They regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical Analysis of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: tuberculosis, WhiB proteins, mycobacterium tuberculosis, nucleic acid binding

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Authors: Ting Zou, Chengfei Zhang

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Objectives: The purpose of this study was to investigate the role of Semaphorin 4D (Sema4D)/Plexin-B1 signaling on osteo/odontogenic differentiation of human dental pulp stem cells (DPSCs) and uncover its molecular mechanism. Methods: DPSCs were cultured in osteo/odontogenic medium. After treatment with Sema4D (10μg/mL), osteo/odontogenic differentiation and mineralization was evaluated by measuring alkaline phosphatase (ALP) activity and alizarin red S staining respectively. The expression of osteo/odontogenic genes (ALP, Col1A1, BSP, and Runx2) was determined by real-time polymerase chain reaction. p-Plexin-B1, Plexin-B1, Col1A1, RhoA, and ErbB2 were analyzed by western. Results: ALP activity and mineralization formation of DPSCs were significantly decreased after treatment with Sema4D (P<0.05). Sema4D significantly down-regulated osteo/odontogenic-related genes expression (ALP, Col1A1, BSP, and Runx2). p-Plexin-B1, Plexin-B1 and RhoA protein expression levels increased after stimulated with Sema4D, while the expression of Col1A1 decreased. Pretreatment with Plexin-B1 antibody blocked Sema4D induced p-Plexin-B1 expression. Conclusion: Sema4D suppressed osteo/odontogenic differentiation of DPSCs via RhoA-mediated pathways.

Keywords: Sema4D/Plexin-B1, dental pulp stem cells, osteo/odontogenic differentiation, alkaline phosphatase (ALP)

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Authors: Emmanuel Flores Huicochea, Guadalupe Borja Mendiola, Jacqueline Flores Lopez, Rodolfo Rendon Villalobos

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The usual procedure to investigate the properties of biodegradable films has been to prepare the film, measure the mechanical or transport properties and then decide whether the mixture has better properties than the individual components, instead of investigating whether the mixture has biopolymer-biopolymer interaction, then prepare the film and finally measure the properties of the film. The work investigates the presence of interaction biopolymer-biopolymer in a mixture of chia biopolymer and gelatin using Laser Confocal Microscopy (LCM). Previously, the chia biopolymer was obtained from chia seed. CML analysis of mixtures of chia biopolymer-gelatin without Na⁺ ions exhibited aggregates of different size, in the range of 100-400 μm, of defined color, for the two colors, but no mixing of color was observed. The increased of gelatin in the mixture decreases the size and number of aggregates. The tridimensional microstructure reveled that there are two layers of biopolymers, chia and gelatin well defined. The mixture chia biopolymer-gelatin with 10 mM Na⁺ and with a ratio 75:25 (chia-gelatin) showed lower aggregated size than others mixture with and without ions. This result could be explained because the chia biopolymer is a polyelectrolyte and the added sodium ions reduce the molecular rigidity by neutralizing the negative charges that the chia biopolymer possesses and therefore a better biopolymer-biopolymer interaction is allowed between the biopolymer of chia and gelatin.

Keywords: biopolymer-biopolymer interaction, confocal laser microscopy, CLM, microstructure, mixture chia-gelatin

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Authors: P. Dubcek, B. Pivac, J. Dasovic, V. Janicki, S. Bernstorff

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When grown only to nanometric sizes, metallic particles (e.g. Ag, Au and Cu) exhibit specific optical properties caused by the presence of plasmon band. The plasmon band represents collective oscillation of the conduction electrons, and causes a narrow band absorption of light in the visible range. When the nanoparticles are embedded in a dielectric, they also cause modifications of dielectrics optical properties. This can be fine-tuned by tuning the particle size. We investigated Cu nanoparticle growth with and without surrounding dielectric (SiO2 capping layer). The morphology and crystallinity were investigated by GISAXS and GIWAXS, respectively. Samples were produced by high vacuum thermal evaporation of Cu onto monocrystalline silicon substrate held at room temperature, 100°C or 180°C. One series was in situ capped by 10nm SiO2 layer. Additionally, samples were annealed at different temperatures up to 550°C, also in high vacuum. The room temperature deposited samples annealed at lower temperatures exhibit continuous film structure: strong oscillations in the GISAXS intensity are present especially in the capped samples. At higher temperatures enhanced surface dewetting and Cu nanoparticles (nanoislands) formation partially destroy the flatness of the interface. Therefore the particle type of scattering is enhanced, while the film fringes are depleted. However, capping layer hinders particle formation, and continuous film structure is preserved up to higher annealing temperatures (visible as strong and persistent fringes in GISAXS), compared to the non- capped samples. According to GISAXS, lateral particle sizes are reduced at higher temperatures, while particle height is increasing. This is ascribed to close packing of the formed particles at lower temperatures, and GISAXS deduced sizes are partially the result of the particle agglomerate dimensions. Lateral maxima in GISAXS are an indication of good positional correlation, and the particle to particle distance is increased as the particles grow with temperature elevation. This coordination is much stronger in the capped and lower temperature deposited samples. The dewetting is much more vigorous in the non-capped sample, and since nanoparticles are formed in a range of sizes, correlation is receding both with deposition and annealing temperature. Surface topology was checked by atomic force microscopy (AFM). Capped sample's surfaces were smoother and lateral size of the surface features were larger compared to the non-capped samples. Altogether, AFM results suggest somewhat larger particles and wider size distribution, and this can be attributed to the difference in probe size. Finally, the plasmonic effect was monitored by UV-Vis reflectance spectroscopy, and relative weak plasmonic effect could be explained by uncomplete dewetting or partial interconnection of the formed particles.

Keywords: coper, GISAXS, nanoparticles, plasmonics

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Authors: Maurizio Dapor, Isabel Abril, Pablo de Vera, Rafael Garcia-Molina

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The ionization yield of ion tracks in polymers and bio-molecular systems reaches a maximum, known as the Bragg peak, close to the end of the ion trajectories. Along the path of the ions through the materials, many electrons are generated, which produce a cascade of further ionizations and, consequently, a shower of secondary electrons. Among these, very low energy secondary electrons can produce damage in the biomolecules by dissociative electron attachment. This work deals with the calculation of the energy distribution of electrons produced by protons in a sample of polymethylmethacrylate (PMMA), a material that is used as a phantom for living tissues in hadron therapy. PMMA is also of relevance for microelectronics in CMOS technologies and as a photoresist mask in electron beam lithography. We present a Monte Carlo code that, starting from a realistic description of the energy distribution of the electrons ejected by protons moving through PMMA, simulates the entire cascade of generated secondary electrons. By following in detail the motion of all these electrons, we find the radial distribution of the energy that they deposit in PMMA for several initial proton energies characteristic of the Bragg peak.

Keywords: Monte Carlo method, secondary electrons, energetic ions, ion-beam cancer therapy, ionization cross section, polymethylmethacrylate, proton beams, secondary electrons, radial energy distribution

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Authors: Aria Vitkova, Hanna Sykulska-Lawrence

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In recent years, Europa has been one of the major focus points in astrobiology due to its high potential of harbouring life in the vast ocean underneath its icy crust. However, the detection of life on Europa faces many challenges due to the harsh environmental conditions and mission constraints. Raman spectroscopy is a highly capable and versatile in-situ characterisation technique that does not require any sample preparation. It has only been used on Earth to date; however, recent advances in optical and laser technology have also allowed it to be considered for extraterrestrial exploration. So far, most efforts have been focused on the exploration of Mars, the most imminent planetary target. However, as an emerging technology with high miniaturization potential, Raman spectroscopy also represents a promising tool for the exploration of Europa. In this study, the capabilities of Raman technology in terms of life detection on Europa are explored and assessed. Spectra of biosignatures identified as high priority molecular targets for life detection on Europa were acquired at various excitation wavelengths and conditions analogous to Europa. The effects of extremely low temperatures and low concentrations in water ice were explored and evaluated in terms of the effectiveness of various configurations of Raman instruments. Based on the findings, a design of a miniaturized Raman instrument optimized for in-situ detection of life on Europa is proposed.

Keywords: astrobiology, biosignatures, Europa, life detection, Raman Spectroscopy

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Authors: Ines Oliveira, Ana Reis

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Magnetic Pulse Welding (MPW) is a cold solid-state welding process, accomplished by the electromagnetically driven, high-speed and low-angle impact between two metallic surfaces. It has the same working principle of Explosive Welding (EXW), i.e. is based on the collision of two parts at high impact speed, in this case, propelled by electromagnetic force. Under proper conditions, i.e., flyer velocity and collision point angle, a permanent metallurgical bond can be achieved between widely dissimilar metals. MPW has been considered a promising alternative to the conventional welding processes and advantageous when compared to other impact processes. Nevertheless, MPW current applications are mostly academic. Despite the existing knowledge, the lack of consensus regarding several aspects of the process calls for further investigation. As a result, the mechanical resistance, morphology and structure of the weld interface in MPW of Al/Cu dissimilar pair were investigated. The effect of process parameters, namely gap, standoff distance and energy, were studied. It was shown that welding only takes place if the process parameters are within an optimal range. Additionally, the formation of intermetallic phases cannot be completely avoided in the weld of Al/Cu dissimilar pair by MPW. Depending on the process parameters, the intermetallic compounds can appear as continuous layer or small pockets. The thickness and the composition of the intermetallic layer depend on the processing parameters. Different intermetallic phases can be identified, meaning that different temperature-time regimes can occur during the process. It is also found that lower pulse energies are preferred. The relationship between energy increase and melting is possibly related to multiple sources of heating. Higher values of pulse energy are associated with higher induced currents in the part, meaning that more Joule heating will be generated. In addition, more energy means higher flyer velocity, the air existing in the gap between the parts to be welded is expelled, and this aerodynamic drag (fluid friction) is proportional to the square of the velocity, further contributing to the generation of heat. As the kinetic energy also increases with the square of velocity, the dissipation of this energy through plastic work and jet generation will also contribute to an increase in temperature. To reduce intermetallic phases, porosity, and melt pockets, pulse energy should be minimized. The bond formation is affected not only by the gap, standoff distance, and energy but also by the mandrel’s surface conditions. No correlation was clearly identified between surface roughness/scratch orientation and joint strength. Nevertheless, the aspect of the interface (thickness of the intermetallic layer, porosity, presence of macro/microcracks) is clearly affected by the surface topology. Welding was not established on oil contaminated surfaces, meaning that the jet action is not enough to completely clean the surface.

Keywords: bonding mechanisms, impact welding, intermetallic compounds, magnetic pulse welding, wave formation

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Authors: Renata Silva-Mann, Sheila Valéria Álvares Carvalho, Robério Anastácio Ferreira, Laura Jane Gomes

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There is growing interest in defining indicators of sustainability, which are important for monitoring the conservation of native forests, particularly in areas of permanent protection. These indicators are references for assessing the state of the forest and the status of the depredated area and its ability to maintain species populations. The aim of the present study was to select genetic parameters as indicators of sustainability for Schinus terebinthifolius Raddi. Fragments located in riparian areas between the Sergipe and Alagoas States in Brazil. This species has been exploited for traditional communities, which represent 20% of the incoming. This study was carried out using the indicators suggested by the Organization for Economic Cooperation and Development, which were identified as Driving-Pressure-State-Impact-Response (DPSIR) factors. The genetic parameters were obtained in five populations located on the shores and islands of the São Francisco River, one of the most important rivers in Brazil. The framework for Schinus conservation suggests seventeen indicators of sustainability. In accordance with genetic parameters, the populations are isolated, and these genetic parameters can be used to monitor the sustainability of those populations in riparian area with the aim of defining strategies for forest restoration.

Keywords: alleles, molecular markers, genetic diversity, biodiversity

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Authors: Shuofeng Yuan, Bojian Zheng

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Assembly of the heterotrimeric polymerase complex of influenza virus from the individual subunits PB1, PA, and PB2 is a prerequisite for viral replication, in which the interaction between the N-terminal of PB1 (PB1N) and the C terminal of PA (PAC) may be a desired target for antiviral development. In this study, we first compared the feasibility of high throughput screening by enzyme-linked immunosorbent assay (ELISA) and fluorescence polarization (FP) assay. Among the two, ELISA was demonstrated to own broader dynamic range so that it was used for screening inhibitors, which blocked PA and PB1 interaction. Several binding inhibitors of PAC-PB1N were identified and subsequently tested for the antiviral efficacy. Apparently, 3-(2-chlorophenyl)-6-ethyl-7-methyl[1,2,4]triazolo[4,3-a]pyrimidin-5-ol, designated ANA-1, was found to be a strong inhibitor of PAC-PB1N interaction and act as a potent antiviral agent against the infections of multiple subtypes of influenza A virus, including H1N1, H3N2, H5N1, H7N7, H7N9 and H9N2 subtypes, in cell cultures. Intranasal administration of ANA-1 protected mice from lethal challenge and reduced lung viral loads in H1N1 virus infected BALB/c mice. Docking analyses predicted that ANA-1 bound to an allosteric site of PAC, which would cause conformational changes thereby disrupting the PAC-PB1N interaction. Overall, our study has identified a novel compound with potential to be developed as an anti-influenza drug.

Keywords: influenza, antiviral, viral polymerase, compounds

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Authors: Christian Röling, Elena Y. Poimanova, Vladimir V. Bruevich

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Here we demonstrate a non-destructive optical technique to localize and characterize single crystals of semiconductive organic materials – Spectroscopic Imaging Ellipsometry. With a combination of microscopy and ellipsometry, it is possible to characterize even micro-sized thin film crystals on plane surface regarding anisotropy, optical properties, crystalline domains and thickness. The semiconducting thiophene-phenylene co-oligomer 1,4-bis(5'-hexyl-[2,2'-bithiophen]-5-yl)benzene (dHex-TTPTT) crystals were grown by solvent based self-assembly technique on silicon substrate with 300 nm thermally silicon dioxide. The ellipsometric measurements were performed with an Ep4-SE (Accurion). In an ellipsometric high-contrast image of the complete sample, we have localized high-quality single crystals. After demonstrating the uniaxial anisotropy of the crystal by using Müller-Matrix imaging ellipsometry, we determined the optical axes by rotating the sample and performed spectroscopic measurements (λ = 400-700 nm) in 5 nm intervals. The optical properties were described by using a Lorentz term in the Ep4-Model. After determining the dispersion of the crystals, we converted a recorded Delta and Psi-map into a 2D thickness image. Based on a quantitative analysis of the resulting thickness map, we have calculated the height of a molecular layer (3.49 nm).

Keywords: anisotropy, ellipsometry, SCFET, thin film

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Authors: Jérôme de Reffye, Marc Antoni

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Following the development of the ERTMS system, we think it is interesting to develop another software-based track circuit system which would fit secondary railway lines with an easy-to-work implementation and a low sensitivity to rail-wheel impedance variations. We called this track circuit 'Track Railway by Automatic Circuits.' To be internationally implemented, this system must not have any mechanical component and must be compatible with existing track circuit systems. For example, the system is independent from the French 'Joints Isolants Collés' that isolate track sections from one another, and it is equally independent from component used in Germany called 'Counting Axles,' in French 'compteur d’essieux.' This track circuit is fully interoperable. Such universality is obtained by replacing the train detection mechanical system with a space-time filtering of train position. The various track sections are defined by the frequency of a continuous signal. The set of frequencies related to the track sections is a set of orthogonal functions in a Hilbert Space. Thus the failure probability of track sections separation is precisely calculated on the basis of signal-to-noise ratio. SNR is a function of the level of traction current conducted by rails. This is the reason why we developed a very powerful algorithm to reject noise and jamming to obtain an SNR compatible with the precision required for the track circuit and SIL 4 level. The SIL 4 level is thus reachable by an adjustment of the set of orthogonal functions. Our major contributions to railway engineering signalling science are i) Train space localization is precisely defined by a calibration system. The operation bypasses the GSM-R radio system of the ERTMS system. Moreover, the track circuit is naturally protected against radio-type jammers. After the calibration operation, the track circuit is autonomous. ii) A mathematical topology adapted to train space localization by following the train through a linear time filtering of the received signal. Track sections are numerically defined and can be modified with a software update. The system was numerically simulated, and results were beyond our expectations. We achieved a precision of one meter. Rail-ground and rail-wheel impedance sensitivity analysis gave excellent results. Results are now complete and ready to be published. This work was initialised as a research project of the French Railways developed by the Pi-Ramses Company under SNCF contract and required five years to obtain the results. This track circuit is already at Level 3 of the ERTMS system, and it will be much cheaper to implement and to work. The traffic regulation is based on variable length track sections. As the traffic growths, the maximum speed is reduced, and the track section lengths are decreasing. It is possible if the elementary track section is correctly defined for the minimum speed and if every track section is able to emit with variable frequencies.

Keywords: track section, track circuits, space-time crossing, adaptive track section, automatic railway signalling

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