Search results for: genomic characterization

Authors: Somia Lakehal Ayat, Ibtissem Samai, Srara Lakehal Ayat, Chaima Dahmani

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The aim of this work relates to the physicochemical diversity and the characterization of the different types of soils of the edough massif (North East of Algeria) and to the evaluation and characterization of the existing organic matter as well as to the evolution. and the dynamics of the latter, also on its influence on changes in the physical properties of soils. In order to know the soil properties of seraidi forest, we established a stratified sampling plan. The results obtained show that we are in the presence of a great diversity of soils, such as neutral to alkaline, whose adsorbent complex is sufficiently saturated. Also, the presence of limestone offers the soil a fairly significant buffering capacity. In our study region, the texture of the soils is varied between clayey and silty, where it offers medium porosity, there is a strong accumulation of organic matter, therefore soils rich in organic matter.The fractionation of the organic matter of the soils allowed to obtain a very high rate of humification. The soil characteristics of the edough massif (North East of Algeria) are controlled by the contribution of organic matter, which presents a dynamic and an important evolution and which varies with the climatic conditions and the nature and the type of plant formation, and these the latter have a capital and important role in the rate of mineralization of organic matter.

Keywords: organic matter, soil, foresty, diversity, mineralization

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Authors: Sai Harshini Irigineni, Suresh Kumar Reddy Narala

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The industrial applicability of aluminium metal matrix composites (AMMCs) has been rapidly growing due to their exceptional materials traits such as low weight, high strength, excellent thermal performance, and corrosion resistance. The increasing demand for AMMCs in automobile, aviation, aerospace and defence ventures has opened up windows of opportunity for the development of processing methods that facilitate low-cost production of AMMCs with superior properties. In the present work, owing to its economy, efficiency, and suitability, powder metallurgy (P/M) technique was employed to develop AMMCs with pure aluminium as matrix material and titanium diboride (TiB₂) as reinforcement. AMMC samples with different weight compositions (Al-0.1%TiB₂, Al-5%TiB₂, Al-10%TiB₂, and Al-15% TiB₂) were prepared through hot press compacting followed by traditional sintering. The developed AMMC was subjected to metallographic studies and mechanical characterization. Experimental evidences show significant improvement in mechanical properties such as tensile strength, hardness with increasing reinforcement content. The current study demonstrates the superiority of AMMCs over conventional metals and alloys and the results obtained may be of immense in material selection for different structural applications.

Keywords: AMMCs, mechanical characterization, powder metallurgy, TiB₂

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: José E. Q. Souza, Marcio Fontana, Antonio C. C. Lima

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This paper presents analysis and characterization of a piezoelectric micro-generator for energy harvesting application. A low-cost experimental prototype was designed to operate as piezoelectric micro-generator in the laboratory. An input acceleration of 9.8m/s2 using a sine signal (peak-to-peak voltage: 1V, offset voltage: 0V) at frequencies ranging from 10Hz to 160Hz generated a maximum average power of 432.4μW (linear mass position = 25mm) and an average power of 543.3μW (angular mass position = 35°). These promising results show that the prototype can be considered for low consumption load application as an energy harvesting micro-generator.

Keywords: piezoelectric, micro-generator, energy harvesting, cantilever beam

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Souhila Bendenia, Chahrazed Bendenia, Hanaa Merad-Dib, Sarra Merabet, Samia Moulebhar, Sid Ahmed Khantar

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Today, environmental pollution is a major concernworldwide, threateninghumanhealth. Various techniques have been used, includingdegradation, filtration, advancedoxidationprocesses, ion exchange, membrane processes, and adsorption. The latter is one of the mostsuitablemethods, usinghighly efficient materials. In this study, NaX zeolite was modified with Cu or Ni at various rates. Following ion exchange, the samples were characterized by XRD, BET and SEM/EDX. After characterization, the exchanged zeolites were used for adsorption of various pollutants as CO2. Different thermodynamic parameters were studied such as Qst. XRD results show that the most intense peaks characteristic of 13X persist after the exchange reaction for all samples. The SEM images of our samples have uniform and regular crystal shapes. The results show that ion exhange with Cu or Ni affect the textural properties of X zeolites and prove that the exchange zeolites can be used as an adsorbent for depollution.

Keywords: X zeolites (NaX), ion exchange, characterization, adsorption

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Authors: Mohamed Mehdi Kadri

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The prediction of hot shale interval in Silurian formation in a well drilled vertically in Ahnet basin Is by logging Data (Resistivity, Gamma Ray, Sonic) with the calculation of total organic carbon (TOC) using ∆ log R Method. The aim of this paper is to present Physico-chemical Properties of Hot Shale using IR spectroscopy and gas chromatography-mass spectrometry analysis; this mixture of measurements, evaluation and characterization show that the hot shale interval located in the lower of Silurian, the molecules adsorbed at the surface of shale sheet are significantly different from petroleum hydrocarbons this result are also supported with gas-liquid chromatography showed that the study extract is a hydroxypropyl.

Keywords: physic-chemical analysis, reservoirs characterization, sweet window evaluation, Silurian shale, Ahnet basin

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Authors: Pablo Raul Yanyachi, Alfredo Mamani Saico, Jorch Mendoza, Wang Xinsheng

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The Attitude Determination and Control System (ADCS) plays a pivotal role in the operation of nanosatellites such as Cubesats, managing orientation and stability during space missions. Within the ADCS, Reaction Wheels (RW) are electromechanical devices responsible for adjusting and maintaining satellite orientation through the application of kinetic moments. This study focuses on the characterization and analysis of a specific Reaction Wheel integrated into an ADCS prototype developed at the National University of San Agust´ın, Arequipa (UNSA). To achieve this, a single-axis Test Bench was constructed, where the reaction wheel consists of a brushless motor and an inertia flywheel driven by an Electronic Speed Controller (ESC). The research encompasses RW characterization, energy consumption evaluation, dynamic modeling, and control. The results have allowed us to ensure the maneuverability of ADCS prototypes while maintaining energy consumption within acceptable limits. The characterization and linearity analysis provides valuable insights for sizing and optimizing future reaction wheel prototypes for nanosatellites. This contributes to the ongoing development of aerospace technology within the scientific community at UNSA.

Keywords: test bench, nanosatellite, control, reaction wheel

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Authors: Mukolwe D. Lubembe, Odongo O. David, Githaka Naftali, Kanduma Esther, Marinda Oosthuizen, Kgomotso P. Sibeko

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Theileriosis is a tick-borne disease of cattle caused by an apicomplexan protozoan parasite of the genus Theileria. In eastern and southern Africa, Theileria infections in cattle are caused by the species Theileria parva whose natural reservoir is the African buffalo (Syncerus caffer). Currently, East Coast Fever (ECF) caused by the cattle-derived Theileria parva is still a major problem in eastern Africa and some parts of southern Africa but not in South Africa following its eradication in the 1950s. However, Corridor disease (CD) caused by the buffalo-derived Theileria parva still remains a concern in South Africa. The diversity of Theileria parva in South Africa in comparison to other affected countries is poorly defined yet its known to be the survival strategy of this parasite. We assessed the antigenic diversity of Theileria parva isolates from Buffalo and cattle at the wildlife-livestock interface comparing samples from South Africa, Zimbabwe, Kenya, Tanzania, and Uganda. Antigenic epitopes of eight schizont antigen genes (Tp1, Tp3, Tp4, Tp5, Tp6, Tp7, Tp8 and Tp10) were amplified by PCR from genomic DNA extracted from blood samples collected from cattle and buffalo at the wildlife-livestock interface. Amplicons were purified and then sequenced on NGS platform. Full length open reading frames (ORFs) of two schizont antigen genes (Tp2 and Tp9) and one sporozoite antigen gene, p67 were also amplified from genomic DNA. Amplicons were then purified and cloned for sequencing. Analysis was based on sequence differences in the genes. Preliminary results show an extensively diverse population of Theileria parva circulating in buffalo and cattle populations at the wildlife-livestock interface. Diversity of the antigen genes contributes to the evasion of the immune system of the host by Theileria parva. This possess a concern in that, some of the Theileria parva populations may re-assort and become adapted to cattle to cause a form of theileriosis that is as fatal as ECF in areas where ECF was eradicated or is absent

Keywords: Theileria parva, east coast fever, corridor diseases, antigen genes, diversity

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Authors: Alok Raghav, Jamal Ahmad

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Background: Serum albumin glycation and advanced glycation end products (AGE) formation correlates in diabetes and its associated complications. Extensive modified human serum albumin is used to study the biochemical, electrochemical and functional properties in hyperglycemic environment with relevance to diabetes. We evaluate Spectroscopic, side chain modifications, amino acid analysis, biochemical and functional group properties in four glucose modified samples. Methods: A series four human serum albumin samples modified with glucose was characterized in terms of amino acid analysis, spectroscopic properties and side chain modifications. The diagnostic technique employed incorporates UV Spectroscopy, Fluorescence Spectroscopy, biochemical assays for side chain modifications, amino acid estimations. Conclusion: Glucose modified human serum albumin confers AGE formation causes biochemical and functional property that depend on the reactivity of glucose and its concentration used for in-vitro glycation. A biochemical and functional characterization of modified albumin in-vitro produced AGE product that will be useful to interpret the complications and pathophysiological significance in diabetes.

Keywords: glycation, diabetes, human serum albumin, biochemical and electrochemical characterization

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Authors: Sandra C. L. Dorea, Joann K. Whalen, Yixin Shao, Oumarou Savadogo

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The major challenge for industries that rely on fossil fuels in manufacturing processes or to provide goods and services is to lower their CO2 emissions, as the case for the manufacture of Portland cement. Feasible materials for this purpose can include agro-industrial or agricultural wastes, which are termed 'biosilica' since the silica was contained in a biological matrix (biomass). Corn cob (CC) has some characteristics that make it a good candidate as biosilica source: 1) it is an abundant grain crop produced around the world; 2) more production means more available residues is left in the field to be used. This work aims to evaluate the CC collected from different farms in Canada during the corn harvest in order to see if they can be used together as a biosilica source. The characterization of the raw CC was made in the physical, chemical, and thermal way. The moisture content, the granulometry, and the morphology were also analyzed. The ash content measured was 2,1%. The Thermogravimetric Analysis (TGA) and its Derivative (DTG) evaluated of CC as a function of weight loss with temperature variation ranging between 30°C and 800°C in an atmosphere of N2. The chemical composition and the presence of silica revealed that the different sources of the CC do not interfere in its basic chemical composition, which means that this kind of waste can be used together as a source of biosilica no matter where they come from. Then, this biosilica can partially replace the cement Portland making sustainable cementitious mixtures and contributing to reduce the CO2 emissions.

Keywords: biosilica, characterization, corn cob, sustainable cementitious materials

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Authors: Aliyu Mohammed Lawal, Dahiru Yau Gital

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The characterisation and the energy potential of the municipal solid wastes in Bauchi town and environs were studied. It was found that, 35,000 tonnes of waste was generated annually at 0.19 kg/capital/day of which, the combination of plastics, rubber, polyethene bags constituted about 33%, followed by textile materials, leathers, wood 26%, combination of papers, cartons 19%, crop stalks/grass 11% and the remaining incombustible materials 11%. The heating value or calorific value of the wastes was determined using a digital calorimeter to be 6.43 MJ/kg, almost one-third of the energy content of peat which has a value of 15.9 MJ/kg. The calorific value of the fuel was found to be significant; hence, the waste could be used for energy generation.

Keywords: calorific value, characterization, digital calorimeter, incombustible, municipal solid waste

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Authors: Aijuka Nicholas

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A research study was undertaken to characterize the aquifers and identify the potential groundwater recharge zones in the Kagandi district. Quantitative characterization of hydraulic conductivities of aquifers is of fundamental importance to the study of groundwater flow and contaminant transport in aquifers. A conditional approach is used to represent the spatial variability of hydraulic conductivity. Briefly, it involves using qualitative and quantitative geologic borehole-log data to generate a three-dimensional (3D) hydraulic conductivity distribution, which is then adjusted through calibration of a 3D groundwater flow model using pumping-test data and historic hydraulic data. The approach consists of several steps. The study area was divided into five sub-watersheds on the basis of artificial drainage divides. A digital terrain model (DTM) was developed using Arc GIS to determine the general drainage pattern of Kagandi watershed. Hydrologic characterization involved the determination of the various hydraulic properties of the aquifers. Potential groundwater recharge zones were identified by integrating various thematic maps pertaining to the digital elevation model, land use, and drainage pattern in Arc GIS and Sufer golden software. The study demonstrates the potential of GIS in delineating groundwater recharge zones and that the developed methodology will be applicable to other watersheds in Uganda.

Keywords: aquifers, Arc GIS, groundwater recharge, recharge zones

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Authors: Miguel A. Campano, Jesica Fernández-Agüera, Samuel Domínguez-Amarillo, Juan J. Sendra

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An analysis of the air tightness level is performed on a representative sample of school classrooms in Southern Spain, which allows knowing the infiltration level of these classrooms, mainly through its envelope, which can affect both energy demand and occupant's thermal comfort. By using a pressurization/depressurization equipment (Blower-Door test), a characterization of 45 multipurpose classrooms have been performed in nine non-university educational institutions of the main climate zones of Southern Spain. In spite of having two doors and a high ratio between glass surface and outer surface, it is possible to see in these classrooms that there is an adequate level of airtightness, since all the n50 values obtained are lower than 9.0 ACH, with an average value around 7.0 ACH.

Keywords: air infiltration, energy efficiency, school buildings, thermal comfort, indoor air quality, ventilation

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Authors: Biruk Wolde, Atalay Ayele, Yonatan Garkabo, Trufat Hailmariam, Zemenu Germewu

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A comprehensive three-dimensional (3D) geological modeling and engineering geological characterization of shallow subsurface soils and rocks are essential for a wide range of geotechnical and seismological engineering applications, particularly in urban environments. The spatial distribution and geological variation of the shallow subsurface of Addis Ababa city have not been studied so far in terms of geological and geotechnical modeling. This study aims at the construction of a 3D geological model, as well as provides awareness into the engineering geological characteristics of shallow subsurface soil and rock of Addis Ababa city. The 3D geological model was constructed by using more than 1500 geotechnical boreholes, well-drilling data, and geological maps. A well-known geostatistical kriging 3D interpolation algorithm was applied to visualize the spatial distribution and geological variation of the shallow subsurface. Due to the complex nature of geological formations, vertical and lateral variation of the geological profiles horizons-solid command has been selected via the Groundwater Modelling System (GMS) graphical user interface software. For the engineering geological characterization of typical soils and rocks, both index and engineering laboratory tests have been used. The geotechnical properties of soil and rocks vary from place to place due to the uneven nature of subsurface formations observed in the study areas. The constructed model ascertains the thickness, extent, and 3D distribution of the important geological units of the city. This study is the first comprehensive research work on 3D geological modeling and subsurface characterization of soils and rocks in Addis Ababa city, and the outcomes will be important for further future research on subsurface conditions in the city. Furthermore, these findings provide a reference for developing a geo-database for the city.

Keywords: 3d geological modeling, addis ababa, engineering geology, geostatistics, horizons-solid

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Authors: D. Jakubowska, M. Malek, P. Wisniewski, J. Mizera, K. J. Kurzydlowski

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The goal of this study was to analyze the technological properties of ceramic slurries based on Ytttria (Y2O3) for fabrication “prime coat” in ceramic shell moulds for investment casting process. The Yttria with two different granulation of (200# and 325#) in ratio-65%-35% by weight were used for preparation the ceramic slurries. Solid phase was 77 wt.%. The experiment was carried out for 96h. Main technological properties like: viscosity, pH, plate weight test, and density were measured every 24h. Additionally, dynamic viscosity was performed after 96h of test. For further material characterization SEM observations, Zeta potential, XRD measurements were done. Those research showed that Yttria ceramic slurries had very promising properties and there are perspective for future fabrication.

Keywords: ceramic slurries, mechanizal properties, viscosity, fabrication

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Authors: Nicole Nazario Bayon, Prathima Prabhu Tumkur, Nithin Krisshna Gunasekaran, Krishnan Prabhakaran, Joseph C. Hall, Govindarajan T. Ramesh

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Titanium nitride (TiN) nanoparticles have sparked interest over the past decade due to their characteristics such as thermal stability, extreme hardness, low production cost, and similar optical properties to gold. In this study, TiN nanoparticles were synthesized via a thermal benzene route to obtain a black powder of nanoparticles. The final product was drop cast onto conductive carbon tape and sputter coated with gold/palladium at a thickness of 4 nm for characterization by field emission scanning electron microscopy (FE-SEM) with energy dispersive X-Ray spectroscopy (EDX) that revealed they were spherical. ImageJ software determined the average size of the TiN nanoparticles was 79 nm in diameter. EDX revealed the elements present in the sample and showed no impurities. Further characterization by X-ray diffraction (XRD) revealed characteristic peaks of cubic phase titanium nitride, and crystallite size was calculated to be 14 nm using the Debye-Scherrer method. Dynamic light scattering (DLS) analysis revealed the size and size distribution of the TiN nanoparticles, with average size being 154 nm. Zeta potential concluded the surface of the TiN nanoparticles is negatively charged. Biocompatibility studies using MTT(3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assay showed TiN nanoparticles are not cytotoxic at low concentrations (2, 5, 10, 25, 50, 75 mcg/well), and cell viability began to decrease at a concentration of 100 mcg/well.

Keywords: biocompatibility, characterization, cytotoxicity, nanoparticles, synthesis, titanium nitride

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Authors: Giang Tran Thi Huong, Hieu Dong Van, Tung Dao Duy, Saadanov Iskender, Isakeev Mairambek, Tsutomu Omatsu, Yukie Katayama, Tetsuya Mizutani, Yuki Ozeki, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Newcastle disease virus (NDV) is a contagious viral disease of the poultry industry and other birds throughout the world. At present, very little is known about molecular epidemiological data regarding the causes of ND outbreak in commercial poultry farms in Kyrgyzstan. In the current study, the NDV isolated from the one out of three samples from the unvaccinated flock was confirmed as NDV. Phylogenetic analysis indicated that this NDV strain is clustered in the Class II subgenotype VIId, and closely related to the Chinese NDV isolate. Phylogenetic analyses revealed that the isolated NDV strain has an origin different from the 4 NDV strains previously identified in Kyrgyzstan. According to the mean death time (MDT: 61.1 h) and a multibasic amino acid (aa) sequence at the F0 proteolytic cleavage site (¹¹²R-R-Q-K-R-F¹¹⁷), the NDV isolate was determined as mesogenic strain. Several mutations in the neutralizing epitopes (notably, ³⁴⁷E→K) and the global head were observed in the hemagglutinin-neuraminidase (HN) protein of the current isolate. The present study represents the molecular characterization of the coding gene region of NDV in Kyrgyzstan. Additionally, further study will be investigated on the antigenic characterization using monoclonal antibody.

Keywords: Kyrgyzstan, Newcastle disease, genotype, genome characterization

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Authors: A. Evcin, N. Çiçek Bezir, R. Duman, N. Duman

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Nowadays, a great concern is placed on the harmfulness of ultraviolet radiation (UVR) which attacks human bodies. Nanocarbon materials, such as carbon nanotubes (CNTs), carbon nanofibers (CNFs) and graphene, have been considered promising alternatives to shielding materials because of their excellent electrical conductivities, very high surface areas and low densities. In the present work, carbon nanofibers have been synthesized from solutions of Polyacrylonitrile (PAN)/ N,N-dimethylformamide (DMF) by electrospinning method. The carbon nanofibers have been stabilized by oxidation at 250 °C for 2 h in air and carbonized at 750 °C for 1 h in H2/N2. We present the fabrication and characterization of transparent and ultraviolet (UV) shielding CNF/polymer composites. The content of CNF filler has been varied from 0.2% to 0.6 % by weight. UV Spectroscopy has been performed to study the effect of composition on the transmittance of polymer composites.

Keywords: electrospinning, carbon nanofiber, characterization, composites, nanofiber, ultraviolet radiation

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Authors: Raffaele A. Calogero

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RNAseq represents an attractive methodology for the detection of functional genomic variants. RNAseq results obtained from polyA+ RNA selection protocol (POLYA) and from exonic regions capturing protocol (ACCESS) indicate that ACCESS detects 10% more coding SNV/INDELs with respect to POLYA. ACCESS requires less reads for coding SNV detection with respect to POLYA. However, if the analysis aims at identifying SNV/INDELs also in the 5’ and 3’ UTRs, POLYA is definitively the preferred method. No particular advantage comes from ACCESS or POLYA in the detection of fusion transcripts.

Keywords: fusion transcripts, INDEL, RNA-seq, WES, SNV

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Authors: Faheema Khan

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To investigate the ability of sensitive and tolerant genotype of Glycine max to adapt to a saline environment in a field, we examined the growth performance, water relation and activities of antioxidant enzymes in relation to photosynthetic rate, chlorophyll a fluorescence, photosynthetic pigment concentration, protein and proline in plants exposed to salt stress. Ten soybean genotypes (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712) were selected and grown hydroponically. After 3 days of proper germination, the seedlings were transferred to Hoagland’s solution (Hoagland and Arnon 1950). The growth chamber was maintained at a photosynthetic photon flux density of 430 μmol m−2 s−1, 14 h of light, 10 h of dark and a relative humidity of 60%. The nutrient solution was bubbled with sterile air and changed on alternate days. Ten-day-old seedlings were given seven levels of salt in the form of NaCl viz., T1 = 0 mM NaCl, T2=25 mM NaCl, T3=50 mM NaCl, T4=75 mM NaCl, T5=100 mM NaCl, T6=125 mM NaCl, T7=150 mM NaCl. The investigation showed that genotype Pusa-24, PK-416 and Pusa-20 appeared to be the most salt-sensitive. genotypes as inferred from their significantly reduced length, fresh weight and dry weight in response to the NaCl exposure. Pusa-37 appeared to be the most tolerant genotype since no significant effect of NaCl treatment on growth was found. We observed a greater decline in the photosynthetic variables like photosynthetic rate, chlorophyll fluorescence and chlorophyll content, in salt-sensitive (Pusa-24) genotype than in salt-tolerant Pusa-37 under high salinity. Numerous primers were verified on ten soybean genotypes obtained from Operon technologies among which 30 RAPD primers shown high polymorphism and genetic variation. The Jaccard’s similarity coefficient values for each pairwise comparison between cultivars were calculated and similarity coefficient matrix was constructed. The closer varieties in the cluster behaved similar in their response to salinity tolerance. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings.Salt tolerant genotype Pusa-37, was further analysed by 2-Dimensional gel electrophoresis to analyse the differential expression of proteins at high salt stress. In the Present study, 173 protein spots were identified. Of these, 40 proteins responsive to salinity were either up- or down-regulated in Pusa-37. Proteomic analysis in salt-tolerant genotype (Pusa-37) led to the detection of proteins involved in a variety of biological processes, such as protein synthesis (12 %), redox regulation (19 %), primary and secondary metabolism (25 %), or disease- and defence-related processes (32 %). In conclusion, the soybean plants in our study responded to salt stress by changing their protein expression pattern. The photosynthetic, biochemical and molecular study showed that there is variability in salt tolerance behaviour in soybean genotypes. Pusa-24 is the salt-sensitive and Pusa-37 is the salt-tolerant genotype. Moreover this study gives new insights into the salt-stress response in soybean and demonstrates the power of genomic and proteomic approach in plant biology studies which finally could help us in identifying the possible regulatory switches (gene/s) controlling the salt tolerant genotype of the crop plants and their possible role in defence mechanism.

Keywords: glycine max, salt stress, RAPD, genomic and proteomic variability

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Authors: Manel Bouloudenine, Karima Djeddou, Hadjer Ben Manser, Hana Soualah Alila, Mohmed Bououdina

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This survey research involves the elaboration and characterization of silver nanoparticles for therapeutic and environmental applications. The silver nanoparticles "Ag NPs" were synthesized by reducing AgNO3 with microwaves. The characterization of nanoparticles was done by using Transmission Electron Microscopy " TEM ", Energy Dispersive Spectroscopy "EDS", Selected Area Electron Diffraction "SEAD", UV-Visible Spectroscopy and Dynamic Light Scattering "DLS". Transmission Electron Microscopy and Electron Diffraction have confirmed the nanoscale, the shape, and the crystalline quality of as synthesized silver nanoparticles. Elementary analysis has proved the purity of Ag NPs and the presence of the Surface Plasmon Resonance phenomenon "SPR". A strong absorption shift was observed in the visible range of the UV-visible spectrum of as synthesized Ag NPs, which indicates the presence of metallic silver. When the strong absorption in the ultraviolet range of the spectrum has revealed the presence of ionic Ag NPs ionic Ag aggregates species. The autocorrelation function measured by the Dynamic Light Scattering has shown a strong monodispersed character of Ag NPs, which is indicated by the presence of a single size population, with a minima and a maxima laying between 40 and 111 nm. Related to other research, our results confirm the performance properties of as synthesized Ag NPs, which allows them to be performing in many technological applications, including therapeutic and environmental ones.

Keywords: silvers nanoparticles, microwaves, EDS, TEM

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Authors: Bensacia Nabila, Hadj-Ziane Amel, Sefah Karima

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Carbon nanocomposites have received more attention in the last years in view of their special properties such as low density, high specific surface area, and thermal and mechanical stability. Taking into account the importance of these materials, many studies aimed at improving the synthesis process have been conducted. However, the presence of impurities could affect significantly the properties of these materials, and the characterization of these compounds is an important challenge to assure the quality of the new carbon nanocomposites. The present study aims to develop a new recyclable decontaminating material for dyes removal. This new material consists of an active element based on carbon nanotubes wrapped in a microcapsule of iron oxide. The adsorbent is characterized by Transmission electron microscopy, X-ray diffraction and the surface area was measured by the BET method.

Keywords: carbon nanocomposite, chitozen, elimination, dyes

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Authors: Najah Majouri, Mohamed El Mankibi, Jalila Sghaier

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This study examined the geotechnical, mineralogical, thermal and physical characterization of clays in south-west Tunisia. Its aims are to elaborate an insulator material based on the clay used in the field of building materials. The geotechnical study showed that the clay studied is characterized by a high degree of plasticity of 30.83%. High mineralogical findings showed that the sample consisted mainly of kaonolite and other clay minerals. The thermal and physical properties of the different samples are obtained by mixing clays, which indicates a promising future for the use of this type of clays in the production of insulating building materials.

Keywords: clay, energy-saving, insulator material, and South-West Tunisia.

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Authors: Nwadike Emmanuel Chinagoron, Achebe Chukwunonso, Ezeliora Chukwuemeka Daniel, Azaka Onyemazuwa Andrew

Abstract:

In this research work, the process of biodiesel production in a pilot plant was studied using cow tallow as raw material, methanol as the solvent and potassium hydroxide as catalysts. The biodiesel quality was determined by characterization. The tallow used in the production had a molecular weight of 860g. Its oil had a density value of 0.8g/ml, iodine value of 63.45, viscosity at 300C was 9.83pas, acid value was 1.96, free fatty acid (FFA) of 0.98%, saponification value of 82.75mleq/kg, specific gravity of 0.898, flash point of 1100C, cloud point of 950C and Calorific value also called Higher Heating Value (HHV) of 38.365MJ/Kg. The produced biodiesel had a density of 0.82g/ml, iodine value of 126.9, viscosity of 4.32pas at 300C, acid value of 0.561, FFA of 0.2805%, saponification value of 137.45 mleq/kg.Flash point, cloud point and centane number of the biodiesel produced are 1390C, 980C and 57.5 respectively, with fat content, protein content, ash content, moisture content, fiber content and carbohydrate content values of 10%, 2.8%, 5%, 5%, 20%, and 37.2% respectively. The biodiesel higher heating values (calorific values) when estimated from viscosity, density and flash points were 41.4MJ/Kg, 63.8MJ/Kg, and 34.6MJ/Kg respectively. The biodiesel was blended with conventional diesel. The blend B-10 had values of 1320C and 960C for flash and cloud points, with Calorific value (or HHV) of 34.6 MJ/Kg (when estimated from its Flash point) and fat content, protein content, ash content, moisture content, fiber content and carbohydrate content values of 5%, 2.1%,10%, 5%, 15%, and 62.9% respectively.

Keywords: biodiesel, characterization, cow-tallow, cetane rating

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Authors: Duy Cuong Nguyen, Ali Makke, Guillaume Montay

Abstract:

This work presents an improved single fiber pull-out test for fiber/matrix interface characterization. This test has been used to study the Inter-Facial Shear Strength ‘IFSS’ of hemp fibers reinforced polypropylene (PP). For this aim, the fiber diameter has been carefully measured using a tomography inspired method. The fiber section contour can then be approximated by a circle or a polygon. The results show that the IFSS is overestimated if the circular approximation is used. The Influence of the molding temperature on the IFSS has also been studied. We find a molding temperature of 183°C leads to better interface properties. Above or below this temperature the interface strength is reduced.

Keywords: composite, hemp, interface, pull-out, processing, polypropylene, temperature

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Authors: Ammar Z. Alshemary, Yi-Fan Goh, Rafaqat Hussain

Abstract:

Magnesium (Mg2+), strontium (Sr2+) and sulphate ions (SO42-) were successfully substituted into hydroxyapatite (Ca10-x-y MgxSry(PO4)6-z(SO4)zOH2-z) structure through ion exchange process at cationic and anionic sites. Mg2+and Sr2+ ions concentrations were varied between (0.00-0.10), keeping concentration of SO42- ions at z=0.05. [Mg (NO3)2], [Sr (NO3)2] and (Na2SO4) were used as Mg2+, Sr2+, and SO42- sources respectively. The synthesized white precipitate were subjected to heat treatment at 500ºC and finally characterized by X-ray diffraction (XRD) and Fourier Transform infra-red spectroscopy (FTIR). The results showed that the substitution of Mg2+, Sr2+ and SO42- ions into the HA lattice resulted in an increase in the broadness and reduction of XRD peaks. This confirmed that the crystallinity was reduced due to the substitution of ions. Similarly, FTIR result showed the effect of substitution on phosphate bands as well as exchange of hydroxyl group by SO42- ions to balance the charges on HA surface.

Keywords: hydroxyapatite, substitution, characterization, XRD, FTIR

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Authors: Mohammed Abdullah Alshahrani

Abstract:

The research focuses on investigating the use of partial least squares (PLS) methodology for addressing challenges associated with high-dimensional correlated data. Recent technological advancements have led to experiments producing data characterized by a large number of variables compared to observations, with substantial inter-variable correlations. Such data patterns are common in chemometrics, where near-infrared (NIR) spectrometer calibrations record chemical absorbance levels across hundreds of wavelengths, and in genomics, where thousands of genomic regions' copy number alterations (CNA) are recorded from cancer patients. PLS serves as a widely used method for analyzing high-dimensional data, functioning as a regression tool in chemometrics and a classification method in genomics. It handles data complexity by creating latent variables (components) from original variables. However, applying PLS can present challenges. The study investigates key areas to address these challenges, including unifying interpretations across three main PLS algorithms and exploring unusual negative shrinkage factors encountered during model fitting. The research presents an alternative approach to addressing the interpretation challenge of predictor weights associated with PLS. Sparse estimation of predictor weights is employed using a penalty function combining a lasso penalty for sparsity and a Cauchy distribution-based penalty to account for variable dependencies. The results demonstrate sparse and grouped weight estimates, aiding interpretation and prediction tasks in genomic data analysis. High-dimensional data scenarios, where predictors outnumber observations, are common in regression analysis applications. Ordinary least squares regression (OLS), the standard method, performs inadequately with high-dimensional and highly correlated data. Copy number alterations (CNA) in key genes have been linked to disease phenotypes, highlighting the importance of accurate classification of gene expression data in bioinformatics and biology using regularized methods like PLS for regression and classification.

Keywords: partial least square regression, genetics data, negative filter factors, high dimensional data, high correlated data

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Authors: Tareg M. Elsunaki, Suleiman A. Arafa, Mohamed A. Abd-Alla

Abstract:

New interesting thermal stable polyesters containing 1-methyl-4-piperidone moiety in the main chain have been synthesized. These polyesters were synthesized by interfacial polycondensation technique of 3,5-bis(4-hydroxybenzylidene)-1-methyl-4-piperidone (I) and 3,5-bis(4-hydroxy-3-methoxy benzyli-dene)-1-methyl-4-piperidone (II) with terphthaloyl, isophthaloyl, 4,4'-diphenic, adipoyl and sebacoyl dichlorides. The yield and the values of the reduced viscosity of the produced polyesters were found to be affected by the type of an organic phase. In order to characterize these polymers, the necessary model compounds (A), (B) were prepared from (I), (II) respectively and benzoyl chloride. The structure of monomers (I), (II), model compounds and resulting polyesters were confirmed by IR, elemental analysis and 1HNMR spectroscopy. The various characteristic of the resulting polymers including solubility, thermal properties, viscosity and X-ray analysis were also studied.

Keywords: synthesis, characterization, new polyesters, chemistry

Procedia PDF Downloads 436