Search results for: genome characterization

Authors: Amtul Jamil Sami

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Apis mellifera is an insect of immense economic importance lives on rich carbohydrate diet including cellulose, nectar, honey and pollen. The carbohydrate metabolism in A mellifera has not been understood fully, as there are no data available, on the functional expression of cellulase gene. The cellulose hydrolyzing enzyme is required for the digestion of pollen cellulose wall, to release the important nutrients (amino acids, minerals, vitamins etc.) from the pollen. A dissection of Apis genome had revealed that there is one gene present for the expression of endo-beta-1,4-glucanase, for cellulose hydrolysis. In the presented work, functional expression of endo-beta-1,4 glucanase gene is reported. Total soluble proteins of the honey bee were isolated and were tested cellulose hydrolyzing enzyme activity, using carboxy-methyl cellulose, as a substrate. A mellifera proteins were able to hydrolyze carboxy-methyl cellulose, confirming its endo- type mode of action. Endo beta-1,4 glucanase enzyme was only present in the gut tissues, no activity was detected in the salivary glands. The pH optima of the enzyme were in the acidic pH range of 4-5-5-0, indicating its metabolic role in the acidic stomach of A mellifera. The reported enzyme is unique, as endo-beta- 1,4 glucanase was able to generate non reducing sugar, as an end product. The results presented, are supportive to the information that the honey bee is capable of producing its novel endo-beta-1,4 glucanase. Further it could be helpful, in understanding, the carbohydrate metabolism in A mellifera.

Keywords: honey bees, Endo-beta 1, 4- glucanase, Apis mellifera, functional expression

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Authors: Kwame Sarkodie, William Cheung, Andrew R. Fergursson

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The characterization of multiphase flow has gained enormous attention for most petroleum and chemical industrial processes. In order to fully characterize fluid phases in a stream or containment, there needs to be a profound knowledge of the existing composition of fluids present. This introduces a problem for real-time monitoring of fluid dynamics such as fluid distributions, and phase fractions. This work presents a simple technique of correlating absorbance spectrums of water, oil and air bubble present in containment. These spectra absorption outputs are derived by using an Fourier Infrared spectrometer. During the testing, air bubbles were introduced into static water column and oil containment and with light absorbed in the infrared regions of specific wavelength ranges. Attenuation coefficients are derived for various combinations of water, gas and oil which reveal the presence of each phase in the samples. The results from this work are preliminary and viewed as a build up to the design of a multiphase flow rig which has an infrared sensor pair to be used for multiphase flow characterization.

Keywords: attenuation, infrared, multiphase, spectroscopy

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Authors: B.Benalioua, I.Benyamina, A.Bentouami, B.Boury

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The objective of this study is based on the synthesis of a new photocatalyst based on TiO2 and its application in the photo-degradation of an acid dye under the visible light. The material obtained was characterized by different techniques like diffuse reflectance UV–Vis spectroscopy (DRS), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The photocatalytic efficiency of the Bi, Zn co-doped TiO2 treated at 670°C for 2 h was tested on the Indigo Carmine under the irradiation of visible light and compared with that of the commercial titanium oxide TiO2-P25 (Degussa). The XRD characterization of the material Bi-Zn-TiO2 (670°C) revealed the presence of the anatase phase and the absence of the rutile phase in comparison of the TiO2 P25 diffractogram. Characterization by UV- visible diffuse reflection (DRS) material showed that the Bi-Zn-TiO2 exhibits redshift (move visible) relative to commercial titanium oxide TiO2-P25, this property promises a photocatalytic activity of Bi-Zn-TiO2 under visible light. Indeed, the efficiency of photocatalytic Bi-Zn-TiO2 as a visible light is shown by a complete discoloration of indigo carmine solution of 16 mg/L after 70 minutes, whereas with the P25-TiO2 discoloration is achieved after 120 minutes.

Keywords: POA, heterogeneous photocatalysis, TiO2, co-doping

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Authors: B. Benalioua, I. Benyamina, A. Bentouami, B. Boury

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The objective of this study is based on the synthesis of a new photocatalyst based on TiO2 and its application in the photo-degradation of an acid dye under the visible light. The material obtained was characterized by different techniques like diffuse reflectance UV–Vis spectroscopy (DRS), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The photocatalytic efficiency of the S, N co-doped TiO2 treated at 600°C for 1 h was tested on the Indigo Carmine under the irradiation of visible light and compared with that of the commercial titanium oxide TiO2-P25 (Degussa). The XRD characterization of the material S-N-TiO2 (600°C) revealed the presence of the anatase phase and the absence of the rutile phase in comparison of the TiO2 P25 diffractogram. Characterization by UV- visible diffuse reflection (DRS) material showed that the S-N-TiO2 exhibits redshift (move visible) relative to commercial titanium oxide TiO2-P25, this property promises a photocatalytic activity of S-N-TiO2 under visible light. Indeed, the efficiency of photocatalytic S-N-TiO2 as a visible light is shown by a complete discoloration of indigo carmine solution of 16 mg/L after 40 minutes, whereas with the P25-TiO2 discoloration is achieved after 90 minutes.

Keywords: POA, heterogeneous photocatalysis, TiO2, co-doping

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Authors: Olga Blagova, Yuliya Osipova, Evgeniya Kogan, Alexander Nedostup

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Purpose: to quantify the value of various clinical, laboratory and instrumental signs in the diagnosis of myocarditis in comparison with morphological studies of the myocardium. Methods: in 100 patients (65 men, 44.7±12.5 years) with «idiopathic» arrhythmias (n = 20) and dilated cardiomyopathy (DCM, n = 80) were performed 71 endomyocardial biopsy (EMB), 13 intraoperative biopsy, 5 study of explanted hearts, 11 autopsy with virus investigation (real-time PCR) of the blood and myocardium. Anti-heart antibodies (AHA) were also measured as well as cardiac CT (n = 45), MRI (n = 25), coronary angiography (n = 47). The comparison group included of 50 patients (25 men, 53.7±11.7 years) with non-inflammatory heart diseases who underwent open heart surgery. Results. Active/borderline myocarditis was diagnosed in 76.0% of the study group and in 21.6% of patients of the comparison group (p < 0.001). The myocardial viral genome was observed more frequently in patients of comparison group than in study group (group (65.0% and 40.2%; p < 0.01. Evaluated the diagnostic value of noninvasive markers of myocarditis. The panel of anti-heart antibodies had the greatest importance to identify myocarditis: sensitivity was 81.5%, positive and negative predictive value was 75.0 and 60.5%. It is defined diagnostic value of non-invasive markers of myocarditis and diagnostic algorithm providing an individual assessment of the likelihood of myocarditis is developed. Conclusion. The greatest significance in the diagnosis of latent myocarditis in patients with 'idiopathic' arrhythmias and DCM have AHA. The use of complex of noninvasive criteria allows estimate the probability of myocarditis and determine the indications for EMB.

Keywords: myocarditis, "idiopathic" arrhythmias, dilated cardiomyopathy, endomyocardial biopsy, viral genome, anti-heart antibodies

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Authors: Suman Singh, Myungho Lee, Insik Park, Yangjai Shin, Youn Suk Lee

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Active antimicrobial films prepared by incorporating AgSiO2, AgZn, and AgZ at 1%, 3%, 5%, 10% (w/w) into polypropylene (PP) matrix. Complete thermal, structural, mechanical and functional characterization were carried out of all formulations and determined the antimicrobial efficiency and returnable antimicrobial efficiency according to the Japanese Industrial Standard method. The morphology of the films showed agglomerates of particles in the composites. The active formulation had decreased elongation compared to the pure PP sample. Thermal analyses indicated that the active formulation compositions had increased thermal stability. The films showed 50% antimicrobial properties after the fifth wash against the tested microorganisms, presenting better activity against Gram negative organisms than Gram positive ones. These findings suggest that PP films with AgSiO2, AgZn, and AgZ particles could provide a significant contribution to the quality and safety of seafood in the distribution chain.

Keywords: antimicrobial film, properties and characterization, returnable packaging, sea food

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Authors: Binder Hans

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Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: Elvira Kusniyanti, Hanni Garminia, Pudji Astuti

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This research studies an interconnection between finitely generated uniform modules and Dedekind prime rings. The characterization of modules over Dedekind prime rings that will be investigated is an adoption of Noetherian and hereditary concept. Dedekind prime rings are Noetherian and hereditary rings. This property of Dedekind prime rings is a background of the idea of adopting arises. In Noetherian area, it was known that a ring R is Noetherian ring if and only if every finitely generated R-module is a Noetherian module. Similar to that result, a characterization of the hereditary ring is related to its projective modules. That is, a ring R is hereditary ring if and only if every projective R-module is a hereditary module. Due to the above two results, we suppose that characterization of a Dedekind prime ring can be analyzed from finitely generated modules over it. We propose a conjecture: a ring R is a Dedekind prime ring if and only if every finitely generated uniform R-module is a Dedekind module. In this article, we will generalize a concept of the Dedekind module for non-commutative ring case and present a part of the above conjecture.

Keywords: dedekind domains, dedekind prime rings, dedekind modules, uniform modules

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Authors: Abdulmalek Marwan Rajkhan, M. S. Al Ghamdi, Mohammed Damoum, Essam Banoqitah

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This paper is about the Am-Be neutron source irradiation of the InP Quantum Dot Laser diode. A QD LD was irradiated for 24 hours and 48 hours. The laser underwent IV characterization experiments before and after the first and second irradiations. A computer simulation using GAMOS helped in analyzing the given results from IV curves. The results showed an improvement in the QD LD series resistance, current density, and overall ideality factor at all measured temperatures. This is explained by the activation of the QD LD Indium composition to Strontium, ionization of the compound QD LD materials, and the energy deposited to the QD LD.

Keywords: quantum dot laser diode irradiation, effect of radiation on QD LD, Am-Be irradiation effect on SC QD LD

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Authors: Jose A. Aznar-Moreno, Xi Jiang, Stefan Burén, Luis M. Rubio

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Integration of prokaryotic nitrogen fixation (nif) genes into the plastid genome for expression of functional nitrogenase components could render plants capable of assimilating atmospheric N2 making their crops less dependent of nitrogen fertilizers. The nitrogenase Fe protein component (NifH) has been used as proxy for expression and targeting of Nif proteins within plant and yeast cells. Here we use tobacco plants with the Azotobacter vinelandii nifH and nifM genes integrated into the plastid genome. NifH and its maturase NifM were constitutively produced in leaves, but not roots, during light and dark periods. Nif protein expression in transplastomic plants was stable throughout development. Chloroplast NifH was soluble, but it only showed in vitro activity when isolated from leaves collected at the end of the dark period. Exposing the plant extracts to elevated temperatures precipitated NifM and apo-NifH protein devoid of [Fe4S4] clusters, dramatically increasing the specific activity of remaining NifH protein. Our data indicate that the chloroplast endogenous [Fe-S] cluster biosynthesis was insufficient for complete NifH maturation, albeit a negative effect on NifH maturation due to excess NifM in the chloroplast cannot be excluded. NifH and NifM constitutive expression in transplastomic plants did not affect any of the following traits: seed size, germination time, germination ratio, seedling growth, emergence of the cotyledon and first leaves, chlorophyll content and plant height throughout development.

Keywords: NifH, chloroplast, nitrogen fixation, crop improvement, transplastomic plants, fertilizer, biotechnology

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Authors: Jialin Ma, Jia Meng

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Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications.

Keywords: RNA-related genomic features, annotation, visualization, web server

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Authors: Arnold I. Malag

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The study wants to establish the data on the characteristics of coastal solid waste in main Island of Masbate as a model for technology interventions. The research utilized the Google Maps to measure the coastal length and Fishbowl Method for area identification. The solid wastes gathered were classified as residual, non-biodegradable, recyclable wastes, and special wastes, based on the waste analysis and characterization manual of Philippine Environmental Governance Project. The wastes were evaluated by weight in kg., dimension in cm., and characteristics as floating or non-floating. Based on the dimension of coastal solid waste, the biodegradable, recyclable, residual and special waste have the average of 40.95 cm., 16.25 cm., 31.37 cm., and 0.725cm. respectively. The waste in the coastal areas is dominated by biodegradable, followed by residual, then recyclable and special wastes with the data of 0.566 kg/m, 0.533 kg/m, 0.114 kg/m and .0007 kg/m respectively. The 97.15% of solid wastes collected is characterized as “floating”, where in the sources are the nearest rivers and waterways and/or the nearest populated areas adjacent to the island. This accumulation of solid wastes can be minimized and controlled by utilizing a floating equipment.

Keywords: solid waste, coastal waste, waste characterization, waste collector

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Authors: Siddhant Sethi, Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto

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Site-directed mutagenesis is a renowned technique to introduce specific mutations in the genome. To achieve site-directed mutagenesis, many chemical and enzymatic approaches have been reported in the past like disulphite induced genome editing, CRISPR-Cas9, TALEN etc. The chemical methods are invasive whereas the enzymatic approaches are time-consuming and expensive. Most of these techniques are unusable in the cellular application due to their toxicity and other limitations. Photo-chemical cytosine deamination, introduced in 2010, is one of the major technique for enzyme-free single-point mutation of cytosine to uracil in DNA and RNA, wherein, 3-cyanovinylcarbazole nucleoside (CNVK) containing oligodeoxyribonucleotide (ODN) having CNVK at -1 position to that of target cytosine is reversibly crosslinked to target DNA strand using 366 nm and then incubated at 90ºC to accommodate deamination. This technique is superior to enzymatic methods of site-directed mutagenesis but has a disadvantage that it requires the use of high temperature for the deamination step which restricts its applicability in the in vivo applications. This study has been focused on improving the technique by reducing the temperature required for deamination. Firstly, the photo-cross-linker, CNVK has been modified by replacing cyano group attached to vinyl group with methyl ester (OMeVK), amide (NH2VK), and carboxylic acid (OHVK) to observe the acceleration in the deamination of target cytosine cross-linked to vinylcarbazole derivative. Among the derivatives, OHVK has shown 2 times acceleration in deamination reaction as compared to CNVK, while the other two derivatives have shown deceleration towards deamination reaction. The trend of rate of deamination reaction follows the same order as that of hydrophilicity of the vinylcarbazole derivatives. OHVK being most hydrophilic has shown highest acceleration while OMeVK is least hydrophilic has proven to be least active for deamination. Secondly, in the related study, the counter-base of the target cytosine, guanine has been replaced by inosine, 2-aminopurine, nebularine, and 5-nitroindole having distinct hydrogen bonding patterns with target cytosine. Among the ODNs with these counter bases, ODN with inosine has shown 12 fold acceleration towards deamination of cytosine cross-linked to CNVK at physiological conditions as compared to guanosine. Whereas, when 2-aminopurine, nebularine, and 5-nitroindole were used, no deamination reaction took place. It can be concluded that inosine has potential to be used as the counter base of target cytosine for the CNVK mediated photo-cross-linking induced deamination of cytosine. The increase in rate of deamination reaction has been attributed to pattern and number of hydrogen bonding between the cytosine and counter base. One of the important factor is presence of hydrogen bond between exo-cyclic amino group of cytosine and the counter base. These results will be useful for development of more efficient technique for site-directed mutagenesis for C → U transformations in the DNA/RNA which might be used in the living system for treatment of various genetic disorders and genome engineering for making designer and non-native proteins.

Keywords: C to U transformation, DNA editing, genome engineering, ultra-fast photo-cross-linking

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Authors: M. F. Elzarei, A. M. Alseaf

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Hundred uncorrelated animal and thirty six markers were used in this study to study the molecular characterization of Saudi native Ardi goat (BM18189, ILSTS030, INRA005, OarFCB48, BM2113, ILSTS033, INRA023, RM088, CSRD247, ILSTS034, INRA063, SRCRSP1, ILSTS002, ILSTS044, INRA172, SRCRSP5, ILSTS005, ILSTS049, MAF70, SRCRSP8, ILSTS011, ILSTS058, OarAE54, SRCRSP9, ILSTS019, ILSTS059, OARCP34, TGLA53, ILSTS022, ILSTS082, OARE129, TGLA73, ILSTS029, ILSTS087, OARE193, and RM004). Ardi goat showed high variability. The mean number of alleles per locus ranged from 5 in SRCRSP1 locus to 13.5 in CSRD247 locus. Gene diversities varied within a wide range, from 0.53 in ILSTS002 locus to 0.86 in RM088 locus. Hardy-Weinberg equilibrium was tested in order to evaluate the significance of inbreeding occurring in each locus in Ardi population. Only SRCRSP9, INRA005, ILSTS030 loci showed significance in this way.

Keywords: molecular characterization, microsatellite markers, Ardi goats, Hardy-Weinberg equilibrium

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Authors: Jose Daniel Giraldo Arias, Camilo Rojas Gomez, David Villegas Delgado, Gullermo Idarraga Alarcon, Juan Meza Meza

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The reverse engineering processes are widely used in the industry with the main goal to determine the materials and the manufacture used to produce a component. There are a lot of characterization techniques and computational tools that are used in order to get this information. A study case of a reverse engineering applied to a secondary sandwich- hybrid type structure used in a helicopter is presented. The methodology used consists of five main steps, which can be applied to any other similar component: Collect information about the service conditions of the part, disassembly and dimensional characterization, functional characterization, material properties characterization and manufacturing processes characterization, allowing to obtain all the supports of the traceability of the materials and processes of the aeronautical products that ensure their airworthiness. A detailed explanation of each step is covered. Criticality and comprehend the functionalities of each part, information of the state of the art and information obtained from interviews with the technical groups of the helicopter’s operators were analyzed,3D optical scanning technique, standard and advanced materials characterization techniques and finite element simulation allow to obtain all the characteristics of the materials used in the manufacture of the component. It was found that most of the materials are quite common in the aeronautical industry, including Kevlar, carbon, and glass fibers, aluminum honeycomb core, epoxy resin and epoxy adhesive. The stacking sequence and volumetric fiber fraction are a critical issue for the mechanical behavior; a digestion acid method was used for this purpose. This also helps in the determination of the manufacture technique which for this case was Vacuum Bagging. Samples of the material were manufactured and submitted to mechanical and environmental tests. These results were compared with those obtained during reverse engineering, which allows concluding that the materials and manufacture were correctly determined. Tooling for the manufacture was designed and manufactured according to the geometry and manufacture process requisites. The part was manufactured and the mechanical, and environmental tests required were also performed. Finally, a geometric characterization and non-destructive techniques allow verifying the quality of the part.

Keywords: reverse engineering, sandwich-structured composite parts, helicopter, mechanical properties, prototype

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Authors: Naima Boudieb, Mohamed Loucif Seaid, Imad Rati, Imane Benammane

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The aim of this study is to synthesis of a copolymer PANI/PEDOT:PSS by electrochemical means to apply in supercapacitors. Polyaniline (PANI) is a conductive polymer; it was synthesized by electrochemical polymerization. It exhibits very stable properties in different environments, whereas PEDOT:PSS is a conductive polymer based on poly(3,4-ethylenedioxythiophene) (PEDOT) and poly(styrene sulfonate)(PSS). It is commonly used with polyaniline to improve its electrical conductivity. Several physicochemical and electrochemical techniques were used for the characterization of PANI/PEDOT:PSS: cyclic voltammetry (VC), electrochemical impedance spectroscopy (EIS), open circuit potential, SEM, X-ray diffraction, etc. The results showed that the PANI/PEDOT:PSS composite is a promising material for supercapacitors due to its high electrical conductivity and high porosity. Electrochemical and physicochemical characterization tests have shown that the composite has high electrical and structural performances, making it a material of choice for high-performance energy storage applications.

Keywords: energy storage, supercapacitors, SIE, VC, PANI, poly(3, 4-ethylenedioxythiophene, PEDOT, polystyrene sulfonate

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Authors: Sridhar A. Malkaram, Tamer E. Fandy

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Purpose: 5-Azacytidine (5AC) and decitabine (DC) are DNA hypomethylating agents. We recently demonstrated that both drugs increase the enzymatic activity of the histone deacetylase enzyme SIRT6. Accordingly, we are comparing the changes H3K9 acetylation changes in the whole genome induced by both drugs using leukemia cells. Description of Methods & Materials: Mononuclear cells from the bone marrow of six de-identified naive acute myeloid leukemia (AML) patients were cultured with either 500 nM of DC or 5AC for 72 h followed by ChIP-Seq analysis using a ChIP-validated acetylated-H3K9 (H3K9ac) antibody. Chip-Seq libraries were prepared from treated and untreated cells using SMARTer ThruPLEX DNA- seq kit (Takara Bio, USA) according to the manufacturer’s instructions. Libraries were purified and size-selected with AMPure XP beads at 1:1 (v/v) ratio. All libraries were pooled prior to sequencing on an Illumina HiSeq 1500. The dual-indexed single-read Rapid Run was performed with 1x120 cycles at 5 pM final concentration of the library pool. Sequence reads with average Phred quality < 20, with length < 35bp, PCR duplicates, and those aligning to blacklisted regions of the genome were filtered out using Trim Galore v0.4.4 and cutadapt v1.18. Reads were aligned to the reference human genome (hg38) using Bowtie v2.3.4.1 in end-to-end alignment mode. H3K9ac enriched (peak) regions were identified using diffReps v1.55.4 software using input samples for background correction. The statistical significance of differential peak counts was assessed using a negative binomial test using all individuals as replicates. Data & Results: The data from the six patients showed significant (Padj<0.05) acetylation changes at 925 loci after 5AC treatment versus 182 loci after DC treatment. Both drugs induced H3K9 acetylation changes at different chromosomal regions, including promoters, coding exons, introns, and distal intergenic regions. Ten common genes showed H3K9 acetylation changes by both drugs. Approximately 84% of the genes showed an H3K9 acetylation decrease by 5AC versus 54% only by DC. Figures 1 and 2 show the heatmaps for the top 100 genes and the 99 genes showing H3K9 acetylation decrease after 5AC treatment and DC treatment, respectively. Conclusion: Despite the similarity in hypomethylating activity and chemical structure, the effect of both drugs on H3K9 acetylation change was significantly different. More changes in H3K9 acetylation were observed after 5 AC treatments compared to DC. The impact of these changes on gene expression and the clinical efficacy of these drugs requires further investigation.

Keywords: DNA methylation, leukemia, decitabine, 5-Azacytidine, epigenetics

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Luz Yoali Alfaro Luna, Angélica Hernández Rayas, Teodoro Córdova Fraga

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This work characterizes and calibrates a fluxgate 539 magnetometer sensor, implementing a real-time monitoring interface to measure magnetic fields with high precision. The objective is to develop an innovative prototype integrating the Fluxgate 539 sensor, a WX-DC2412 power supply, and an Arduino UNO. Methods include interface programming and data conversion to Gauss units. The results show accurate measurements after calibrating the sensor, establishing a foundation for further research in magnetobiology.

Keywords: calibration, fluxgate 539, magnetobiology, magnetic field measurement, monitoring interface, sensor characterization

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Authors: Micheale Yifter Weldemichael

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

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Authors: Ana Paula Gomes Nogueira, Pietro Tonolini, Andrea Bonfanti

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Automotive braking systems must convert kinetic into thermal energy by friction. Nowadays, the disc brake system is the most widespread configuration on the automotive market, which its specific configuration provides a very efficient heat dissipation. At the same time, both discs and pads wear out. Different wear mechanisms can act during the braking, which makes the understanding of the phenomenon essential for the strategies to be applied when an increased lifetime of the components is required. In this study, a specific characterization approach was conducted to analyze the worn surfaces of commercial pad friction materials and its conterface cast iron disc after dynobench tests. Scanning electronic microscope (SEM), confocal microscope, and focus ion beam microscope (FIB) were used as the main tools of the analysis, and they allowed imaging of the footprint of the different wear mechanisms presenting on the worn surfaces. Aspects such as the temperature and specific ingredients of the pad friction materials are discussed since they play an important role in the wear mechanisms.

Keywords: wear mechanism, surface characterization, brake tests, friction materials, disc brake

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

Abstract:

Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

Procedia PDF Downloads 591

Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

Abstract:

Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

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Authors: Nadjette Belhamra, Abdelouahed Chala, Ibrahim Guasmi

Abstract:

Titanium nitride coatings have been extensively used in industry, such as in cutting tools. TiN coating were deposited by chemical vapour deposition (CVD) on carbide insert at a temperature between 850°C and 1100°C, which often exceeds the hardening treatment temperature of the metals. The objective of this work is to realize, to characterize of TiN coating and to apply it in the turning of steel 42CrMo4 under lubrification. Various experimental techniques were employed for the microstructural characterization of the coatings, e. g., X-ray diffraction (XRD), scanning electron microscope (SEM) model JOEL JSM-5900 LV, equipped with energy dispersive X-ray (EDX). The results show that TiN-coated demonstrate a good wear resistance.

Keywords: hard coating TiN, carbide inserts, machining, turning, wear

Procedia PDF Downloads 552

Authors: Nadeem A. Kizilbash

Abstract:

The study aimed to compare the histopathological characterization of prostate cancer using the conventional and 2005 ISUP modified Gleason system. It employed samples from 40 prostate cancer patients employing resection, biopsies and RP. The majority of cases (95%) comprised adenocarcinoma of the prostate. The results showed that there is migration or upgrading of scores to higher values on using the 2005 ISUP modified Gleason system and an increase in a score of 7 in more than 45% of the cases.

Keywords: prostate cancer, conventional gleason grading, 2005 ISUP modified gleason system, histopathology

Procedia PDF Downloads 425

Authors: J. Ivorra-Martinez, L. Quiles-Carrillo, J. Gomez-Caturla, T. Boronat, R. Balart

Abstract:

The utilization of almond crop by-products to obtain PHBH-based composites was carried out by using an extrusion process followed by an injection to obtain test samples. To improve the properties of the resulting composite, the incorporation of OLA 8 as a coupling agent and plasticizer was additionally considered. A characterization process was carried out by the measurement of mechanical properties, thermal properties, surface morphology, and water absorption ability. The use of the almond residue allows obtaining composites based on PHBH with a higher environmental interest and lower cost.

Keywords: almond shell, PHBH, composites, compatibilization

Procedia PDF Downloads 101

Authors: Babak Eslami

Abstract:

Bimodal and trimodal AFM have provided additional capabilities to scanning probe microscopy characterization techniques. These capabilities have specifically enhanced material characterization of surfaces and provided subsurface imaging in addition to conventional topography images. Bimodal and trimodal AFM, being different techniques of multifrequency AFM, are based on exciting the cantilever’s fundamental eigenmode with second and third eigenmodes simultaneously. Although higher eigenmodes provide a higher number of observables that can provide additional information about the sample, they cause experimental challenges. In this work, different experimental approaches for enhancing AFM images in multifrequency for different characterization goals are provided. The trade-offs between eigenmodes including the advantages and disadvantages of using each mode for different samples (ranging from stiff to soft matter) in both air and liquid environments are provided. Additionally, the advantage of performing conventional single tapping mode AFM with higher eigenmodes of the cantilever in order to reduce sample indentation is discussed. These analyses are performed on widely used polymers such as polystyrene, polymethyl methacrylate and air nanobubbles on different surfaces in both air and liquid.

Keywords: multifrequency, sensitivity, soft matter, polymer

Procedia PDF Downloads 132

Authors: Amit Keshav

Abstract:

Waste bone, produced in large quantity (8-10 kg./day) from a slaughterhouse, could be a cheap (cost $0.20 per kg) substitute for commercial catalysts. In the present work, catalyst for esterification reaction was prepared from waste bone and characterized by various techniques. Bone was deoiled and then sulfonated. Fourier-transform infrared spectroscopy (FTIR) spectra of prepared catalyst predicted –OH vibration at 3416 and 1630 cm⁻¹, S-O stretching at 1124 cm⁻¹ and intense bands of hydroxypatite in a region between 500 and 700 cm⁻¹. X-ray diffraction (XRD) predicts peaks of hydroxyapatite, CaO, and tricalcium phosphate. Scanning electron microscope (SEM) was employed to reveal the presence of non-uniformity deposited fine particles on the catalyst surface that represents active acidic sites. The prepared catalyst was employed to study its performance on esterification reaction between acrylic acid and ethanol in a molar ratio of 1:1 at a set temperature of 60 °C. Results show an equilibrium conversion of 49% which is matched to the commercial catalysts employed in literature. Thus waste bone could be a good catalyst for acrylic acid removal from waste industrial streams via the process of esterification.Keywords— Heterogeneous catalyst, characterization, esterification, equilibrium conversion

Keywords: heterogeneous catalyst, characterization, esterification, equilibrium conversion

Procedia PDF Downloads 141

Authors: M. Hadji, N. Chiker, Y. Hadji, A. Haddad

Abstract:

In this paper, we report for the first time on the synthesis and characterization of novel MAX phases (Ti3SiC2, Ti2AlC) reinforced Ni-matrix and Ti2AlC reinforced Al-matrix. The stability of MAX phases in Al-matrix and Ni-matrix at a temperature of 985°C has been investigated. All the composites were cold pressed and sintered at a temperature of 985°C for 20min in H2 environment, except (Ni/Ti3SiC2) who was sintered at 1100°C for 1h.Microstructure analysis by scanning electron microscopy and phase analysis by X-Ray diffraction confirmed that there was minimal interfacial reaction between MAX particles and Ni, thus Al/MAX samples shown that MAX phases was totally decomposed at 985°C.The Addition of MAX enhanced the Al-matrix and Ni-matrix.

Keywords: MAX phase, microstructures, composites, hardness, SEM

Procedia PDF Downloads 345

Authors: Mian Gul Sayed, Rahim Shah, Fazal Mabood, Najeeb Ur Rahman, Maher Noor

Abstract:

Embarking on the frontier of molecular advancement, this study focuses on the synthesis and characterization of a distinct class of porphyrin derivatives—specifically, the 5, 10, 15, 20-tetrakis (3-bromopropoxyphenyl) porphyrins. Through meticulous synthetic methodologies, these derivatives are crafted, strategically incorporating bromopropoxyphenyl moieties at distinct positions within the porphyrin framework. This research aims to unravel the structural intricacies and explore the potential applications of these compounds through a detailed characterization utilizing advanced analytical techniques. 5, 10, 15, 20, tetrakis (4-hydroxyphenyl) porphyrin was synthesized by treating pyrrole and p- hydroxylbenzaldehyde. 5, 10, 15, 20, tetrakis-(4-hydroxyphenyl) was converted into 5, 10, 15, 20, tetrakis (4-bromoalkoxyphenyl) porphyrin. 5,10,15, 20-Tetrakis -(4-bromoalkoxyphenyl) porphyrin was treated with Isopropyl phenol, para-Aminophenol, hydroquinone, 2-Naphthol, 1-Naphthol and Hydroquinone and different derivatives of ether-linked were obtained. The synthesized compounds were analyzed using contemporary spectroscopic techniques like UV-Vis, NMR and Mass spectrometry. The synthesized compounds were also tested for their biological activities like antioxidants and anti-inflammatory.

Keywords: tetraphenyl porphyrin, NMR, antioxidant, anti-inflammatory

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