Search results for: material genome

Authors: Yong-Jun Jeon, Hyung-Pil Park, Min-Jae Song, Baeg-Soon Cha

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Following the recent trend of having increased demand in producing lighter-weight car bodies for improvement of automobile safety and gas mileage, there is a forming method that makes use of hot-stamping technique, which satisfies all conditions mentioned above. Hot-stamping is a forming technique with advantages of excellent formability, good dimensional precision and others since it is a process in which steel plates are heated up to temperatures of at least approximately 900°C after which forming is conducted in die at room temperature followed by rapid cooling. In addition, it has characteristics of allowing for improvement in material strength through achievement of quenching effect by having simultaneous forming and rapid cooling of material of high temperatures. However, there is insufficient information on the changes in material strength according to changes in material temperature with regards to material heating method and forming process in hot-stamping. Accordingly, this study aims to design and press die for T-type product of the scale models of the center pillar and to understand the changes in material strength in relation to changes in forming methods of hot-stamping process. Thus in order to understand the changes in material strength due to quenching effect among the hot-stamping process, material strength and material forming precision were to be studied while varying the forming and forming method when forming. For test methods, material strength was observed by using boron steel that has boron additives, which was heated up to 950°C, after which it was transferred to a die and was cooled down to material temperature of 400°C followed by air cooling process. During the forming and cooling process here, experiment was conducted with forming parameters of 2 holding rates and 3 flange heating rates wherein changing appearance in material strength according to changes forming method were observed by verifying forming strength and forming precision for each of the conditions.

Keywords: hot-stamping, formability, quenching, forming, press die, forming methods

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Authors: Jasna Prester, Najla Podrug, Davor Filipović

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Manufacturing companies invest a significant amount of sales into material resources for production. In our sample, 58% of sales is used for manufacturing inputs, while only 24% of sales is used for salaries. This means that if a company is looking to reduce costs, the greater potential is in reduction of material costs than downsizing. This research shows that manufacturing companies in Croatia did realize material savings in last three years. It is also shown by which technologies they achieved materials cost savings. Through literature research, we found research gap as to which technologies reduce material consumption. As methodology of research four regression analyses are used to prove our findings.

Keywords: Croatia, materials savings strategies, technologies, return on sales

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Authors: O. Eren, L. Zakar

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Recycling steel building components is key to the sustainability of a structure’s end-of-life, as it is the most economical solution. In this paper the effects of usage of recycled steel material in tall buildings aspects are investigated.

Keywords: building, recycled material, steel, structure

Procedia PDF Downloads 359

Authors: Sumeet Rai, Anuj Tyagi, B. T. Naveen Kumar, Shubhkaramjeet Kaur, Niraj K. Singh

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Since their discovery, indiscriminate use of antibiotics in human, veterinary and aquaculture systems has resulted in global emergence/spread of multidrug-resistant bacterial pathogens. Thus, the need for alternative approaches to control bacterial infections has become utmost important. High selectivity/specificity of bacteriophages (phages) permits the targeting of specific bacteria without affecting the desirable flora. In this study, a lytic phage (Ahp1) specific to Aeromonas hydrophila subsp. hydrophila was isolated from finfish aquaculture pond. The host range of Ahp1 range was tested against 10 isolates of A. hydrophila, 7 isolates of A. veronii, 25 Vibrio cholerae isolates, 4 V. parahaemolyticus isolates and one isolate each of V. harveyi and Salmonella enterica collected previously. Except the host A. hydrophila subsp. hydrophila strain, no lytic activity against any other bacterial was detected. During the adsorption rate and one-step growth curve analysis, 69.7% of phage particles were able to get adsorbed on host cell followed by the release of 93 ± 6 phage progenies per host cell after a latent period of ~30 min. Phage nucleic acid was extracted by column purification methods. After determining the nature of phage nucleic acid as dsDNA, phage genome was subjected to next-generation sequencing by generating paired-end (PE, 2 x 300bp) reads on Illumina MiSeq system. De novo assembly of sequencing reads generated circular phage genome of 42,439 bp with G+C content of 58.95%. During open read frame (ORF) prediction and annotation, 22 ORFs (out of 49 total predicted ORFs) were functionally annotated and rest encoded for hypothetical proteins. Proteins involved in major functions such as phage structure formation and packaging, DNA replication and repair, DNA transcription and host cell lysis were encoded by the phage genome. The complete genome sequence of Ahp1 along with gene annotation was submitted to NCBI GenBank (accession number MF683623). Stability of Ahp1 preparations at storage temperatures of 4 °C, 30 °C, and 40 °C was studied over a period of 9 months. At 40 °C storage, phage counts declined by 4 log units within one month; with a total loss of viability after 2 months. At 30 °C temperature, phage preparation was stable for < 5 months. On the other hand, phage counts decreased by only 2 log units over a period of 9 during storage at 4 °C. As some of the phages have also been reported as glycerol sensitive, the stability of Ahp1 preparations in (0%, 15%, 30% and 45%) glycerol stocks were also studied during storage at -80 °C over a period of 9 months. The phage counts decreased only by 2 log units during storage, and no significant difference in phage counts was observed at different concentrations of glycerol. The Ahp1 phage discovered in our study had a very narrow host range and it may be useful for phage typing applications. Moreover, the endolysin and holin genes in Ahp1 genome could be ideal candidates for recombinant cloning and expression of antimicrobial proteins.

Keywords: Aeromonas hydrophila, endolysin, phage, narrow host range

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Authors: Timur Mukhametkaliyev

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The earthen material possesses low compression strength, and it is highly sensitive to the water content. Different binders can be added (Portland cement or lime) to improve the durability and the mechanical characteristics of earthen material, but the production of these binders has high embodied energy and results in an increase in world CO₂ emission. Geopolymers are binders which can be synthesized at low temperature in alkaline solutions from raw materials consisting of amorphous aluminosilicates. Geopolymers are an attractive substitution of Portland cement and can be used as an excellent stabilization for earthen material. In this study, earthen material stabilized with geopolymer binder for use in construction 3D printing was developed. Construction 3D printing offers freedom of design, waste minimisation, customisation, reduced labour, and automation. For successful 3D printing, the properties of used material are the most important aspects because they require adaptability for extrusion and controlled time of hardening for the binder.

Keywords: 3D printing, building construction, geopolymer, architecture

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Authors: Moulay Smaïne Ghembaza, Mokhtar Dadouch, Nour-Said Ikhlef

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Soil treatment is to make use soil that does not have the characteristics required in a given context. We limit ourselves in this work to the field of road earthworks where we have chosen to develop a local material in the region of Sidi Bel Abbes (Algeria). This material has poor characteristics not meeting the standards used in road geo technics. To remedy this, firstly, we were trying to improve the Proctor Standard characteristics of this material by mechanical treatment increasing the compaction energy. Then, by a chemical treatment, adding some cement dosages, our results show that this material classified A1h a increase maximum dry density and a reduction in the water content of compaction. A comparative study is made on the optimal properties of the material between the two modes of treatment. On the other hand, after treatment, one finds a decrease in the plasticity index and the methylene blue value. This material exhibits a change of class. Therefore, soil class CL turned into a soil class composed CL-ML (Silt of low plasticity). This observation allows this material to be used as backfill or sub grade.

Keywords: treatment of soil, cement, subgrade, Atteberg limits, classification, optimum proctor properties

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Authors: Shama, Asif Mahmood, Wen Zhang

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Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to library construction, which were then sequenced on the Illumina MiSeq platform. The sequenced reads were analyzed using a viral metagenomic analysis pipeline. A cardiovirus from the feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on the P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats, which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

Keywords: cardioviruses, viral metagenomics, novel viruses, virus-host interaction

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Authors: Jingyuan Hu, Zhandong Liu

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CRISPR genome editing technology has transformed molecular biology by accurately targeting and altering an organism’s DNA. Despite the state-of-art precision of CRISPR genome editing, the imprecise mutation outcome and off-target effects present considerable risk, potentially leading to unintended genetic changes. Targeted deep sequencing, combined with bioinformatics sequence alignment, can detect such unwanted mutations. Nevertheless, the classical method, Needleman-Wunsch (NW) algorithm may produce false alignment outcomes, resulting in inaccurate mutation identification. The key to precisely identifying CRISPR-induced mutations lies in determining optimal parameters for the sequence alignment algorithm. Hidden Markov models (HMM) are ideally suited for this task, offering flexibility across CRISPR systems by leveraging forward-backward algorithms for parameter estimation. In this study, we introduce CRISPR-HMM, a statistical software to precisely call CRISPR-induced mutations. We demonstrate that the software significantly improves precision in identifying CRISPR-induced mutations compared to NW-based alignment, thereby enhancing the overall understanding of the CRISPR gene-editing process.

Keywords: CRISPR, HMM, sequence alignment, gene editing

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Authors: Santhita Tungkajiwangkoon, Yoshikazu Hoshi

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Three Japaneses Drosera species are the good model to study genome organization with highly specialized morphological group for insect trapping, and has revealed anti-inflammatory, and antibacterial effects, so there must be a reason for botanists are so appealing in these plants. Cytology and Flow cytometry were used to investigate the genetic stability and ploidy estimation in three related species. The cytological and Flow cytometry analysis were done in Drosera rotundifolia L., Drosera spatulata Labill and Drosera tokaiensis. The cytological studies by fluorescence staining (DAPI) showed that D. tokaiensis was an alloploid (2n=6x=60, hexaploid) which is a natural hybrid polyploids of D. rotundifolia and D. spatulata. D. rotundifolia was a diploid with the middle size of metaphase chromosomes (2n=2x=20) as a paternal origin and D. spatulata was a tetraploid with small size of metaphase chromosome (2n=4x=40) as a maternal origin. We confirmed by Flow cytometry analysis to determine the ploidy level and DNA content of the plants. The 2C-DNA values of D. rotundiflolia were 2.8 pg, D. spatulata was 1.6 pg and D. tokaiensis was 3.9 pg. However, 2C- DNA values of D. tokaiensis should be related from their parents but in the present study the 2C-DNA values of D. tokaiensis was no relation from the theoretical of hybrids representing additive parental. Possibility of D. tokaiensis is a natural hybrid, which is also hybridization in natural evolution can cause the genome reduction in plant.

Keywords: drosera, hybrid, cytology, flow cytometry

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Authors: Tahani Farah, Hanène Souli, Jean-Marie Fleureau, Guillaume Kermouche, Jean-Jacques Fry, Benjamin Girard, Denis Aelbrecht

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In this work, the bio-clogging of two soils with different granulometries is presented. The durability of the clogging is also studied under cycles of hydraulic head and under cycles of desaturation- restauration. The studied materials present continuous grain size distributions. The first one corresponding to the "material 1", presents grain sizes between 0.4 and 4 mm. The second material called "material 2" is composed of grains with size varying between 1 and 10 mm. The results show that clogging occurs very quickly after the injection of nutrition and an outlet flow near to 0 is observed. The critical hydraulic head is equal to 0.76 for "material 1", and 0.076 for "material 2". The durability tests show a good resistance to unclogging under cycles of hydraulic head and desaturation-restauration for the "material 1". Indeed, the flow after the cycles is very low. In contrast, "material 2", shows a very bad resistance, especially under the hydraulic head cycles. The resistance under the cycles of desaturation-resaturation is better but an important increase of the flow is observed. The difference of behavior is due to the granulometry of the materials. Indeed, the large grain size contributes to the reduction of the efficiency of the bio-clogging treatment in this material.

Keywords: bio-clogging, granulometry, permeability, nutrition

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Authors: S. Najafi, E. Bertini, M. Pezzotti, G.B. Tornielli, S. Zenoni

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Grapevine is an important agricultural fruit crop plant consumed worldwide and with a key role in the global economy. Grapevine is strongly affected by both biotic and abiotic stresses, which impact grape growth at different stages, such as during plant and berry development and pre- and post-harvest, consequently causing significant economic losses. Recently global warming has propelled the anticipation of the onset of berry ripening, determining the reduction of a grape color and increased volatilization of aroma compounds. Climate change could negatively alter the physiological characteristics of the grape and affect the berry and wine quality. Modern plant breeding can provide tools such as genome editing for improving grape resilience traits while maintaining intact the viticultural and oenological quality characteristics of the genotype. This study aims at developing a platform for genome editing application in grapevine plants with the final goal to improve berry quality, biotic, and abiotic resilience traits. We chose to directly deliver ribonucleoproteins (RNP, preassembled Cas protein and guide RNA) into plant protoplasts, and, from these cell structures, regenerate grapevine plants edited in specific selected genes controlling traits of interest. Edited plants regenerated by somatic embryogenesis from protoplasts will then be sequenced and molecularly characterized. Embryogenic calli of Sultana and Shiraz cultivars were initiated from unopened leaves of in-vitro shoot tip cultures and from stamens, respectively. Leaves were placed on NB2 medium while stamens on callus initiation medium (PIV) medium and incubated in the dark at 28 °C for three months. Viable protoplasts, tested by FDA staining, isolated from embryogenic calli were cultured by disc method at 1*105 protoplasts/ml. Mature well-shaped somatic embryos developed directly in the protoplast culture medium two months later and were transferred in the light into to shooting medium for further growth. Regenerated plants were then transferred to the greenhouse; no phenotypic alterations were observed when compared to non in-vitro cultured plants. The performed experiments allowed to established an efficient protocol of embryogenic calli production, protoplast isolation, and regeneration of the whole plant through somatic embryogenesis in both Sultana and Shiraz. Regenerated plants, through direct somatic embryogenesis deriving from a single cell, avoid the risk of chimerism during the regeneration process, therefore improving the genome editing process. As pre-requisite of genome editing, an efficient method for transfection of protoplast by yellow fluorescent protein (YFP) marker genes was also established and experiments of direct delivery of CRISPR–Cas9 ribonucleoproteins (RNPs) in protoplasts to achieve efficient DNA-free targeted mutations are in progress.

Keywords: CRISPR-cas9, plant regeneration, protoplast isolation, Vitis vinifera

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: Yugander Arra, Florence Auguy, Melissa Stiebner, Sophie Chéron, Michael M. Wudick, Van Schepler-Luu, Sébastien Cunnac, Wolf B. Frommer, Laurence Albar

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Rice yellow mottle virus (RYMV) is one of the most important diseases affecting rice in Africa. The most promising strategy to reduce yield losses is the use of highly resistant varieties. The resistance gene RYMV2 is homolog of the Arabidopsis constitutive expression of pathogenesis related protein-5 (AtCPR5) nucleoporin gene. Resistance alleles are originating from African cultivated rice Oryza glaberrima, rarely cultivated, and are characterized by frameshifts or early stop codons, leading to a non-functional or truncated protein. Rice possesses two paralogs of CPR5 and function of these genes are unclear. Here, we evaluated the role of the two rice candidate nucleoporin paralogs OsCPR5.1 (pathogenesis-related gene 5; RYMV2) and OsCPR5.2 by CRISPR/Cas9 genome editing. Despite striking sequence and structural similarity, only loss-of-function of OsCPR5.1 led to full resistance, while loss-of-function oscpr5.2 mutants remained susceptible. Short N-terminal deletions in OsCPR5.1 also did not lead to resistance. In contrast to Atcpr5 mutants, neither OsCPR5.1 nor OsCPR5.2 knock out mutants showed substantial growth defects. Taken together, the candidate nucleoporin OsCPR5.1, but not its close homolog OsCPR5.2, plays a specific role for the susceptibility to RYMV, possibly by impairing the import of viral RNA or protein into the nucleus. Whereas gene introgression from O. glaberrima to high yielding O. sativa varieties is impaired by strong sterility barriers and the negative impact of linkage drag, genome editing of OsCPR5.1, while maintaining OsCPR5.2 activity, thus provides a promising strategy to generate O. sativa elite lines that are resistant to RYMV.

Keywords: CRISPR Cas9, genome editing, knock out mutant, recessive resistance, rice yellow mottle virus

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: Narin Salehiyan

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The later sequencing of the complete genomes of Mycoplasma genitalium and M. pneumoniae has pulled in significant consideration to the atomic science of mycoplasmas, the littlest self-replicating living beings. It shows up that we are presently much closer to the objective of defining, in atomic terms, the complete apparatus of a self-replicating cell. Comparative genomics based on comparison of the genomic cosmetics of mycoplasmal genomes with those of other microbes, has opened better approaches of looking at the developmental history of the mycoplasmas. There's presently strong hereditary bolster for the speculation that mycoplasmas have advanced as a department of gram-positive microbes by a handle of reductive advancement. Amid this prepare, the mycoplasmas misplaced significant parcels of their ancestors’ chromosomes but held the qualities basic for life. In this way, the mycoplasmal genomes carry a tall rate of preserved qualities, incredibly encouraging quality comment. The critical genome compaction that happened in mycoplasmas was made conceivable by receiving a parasitic mode of life. The supply of supplements from their has clearly empowered mycoplasmas to lose, amid advancement, the qualities for numerous assimilative forms. Amid their advancement and adjustment to a parasitic mode of life, the mycoplasmas have created different hereditary frameworks giving a profoundly plastic set of variable surface proteins to avoid the have safe framework.

Keywords: mycoplasma, plasma, pathogen, genome

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Authors: Mohammad Saleem, Mujahid Kamran

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It is shown that causality, the principle that cause must precede effect, leads inter alia, to highly significant result that the velocity of a material particle cannot be even equal to that of light. Consequently, combined with special relativity, it leads to the conclusion that material particles of zero rest mass cannot exist in nature. Thus, causality, a principle without which nature would be incomprehensible, combined with special relativity, forbids the existence of material particles of zero rest mass. For instance, the neutrinos, as is now known, are material particles of non-zero rest mass. The situation changes when we consider the gauge particles. In fact, when the principle of causality was proposed, the concept of gauge particles had not yet been introduced. Now we know that photon, a gauge particle with zero rest mass does exist in nature. Therefore, principle of causality, as generally stated, is valid only for material particles. For gauge particles, in order to make the statement of causality consistent with experiment, it has to be modified: The cause should either precede or be simultaneous with the effect. Combined with special relativity, it allows gauge particles of zero rest mass.

Keywords: causality, gauge particles, material particles, special relativity

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Authors: Rofida Gamal, Mostafa Mohammed, Mariam Adel, Marwa Gamal, Marwa kamal, Ayat Saber, Maha Mamdouh, Amira Emad, Mai Ramadan

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Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations.

Keywords: Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers

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Authors: Yiğit Gürler, İbrahim Şimşek, Müge Savaştaer, Ayberk Karakuş, Alper Taşdemirci

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316L steel is frequently used in the industry due to its easy formability and accessibility in sheet metal forming processes. Numerical and experimental studies are frequently encountered in the literature to examine the mechanical behavior of 316L stainless steel during the forming process. 316L stainless steel is the most common material used in the production of plate heat exchangers and plate heat exchangers are produced by plastic deformation of the stainless steel. The motivation in this study is to determine the appropriate material model during the simulation of the sheet metal forming process. For this reason, two different material models were examined and Ls-Dyna material cards were created using material test data. These are MAT133_BARLAT_YLD2000 and MAT093_SIMPLIFIED_JOHNSON_COOK. In order to compare results of the tensile test & hydraulic bulge test performed both numerically and experimentally. The obtained results were evaluated comparatively and the most suitable material model was selected for the forming simulation. In future studies, this material model will be used in the numerical modeling of the sheet metal forming process.

Keywords: 316L, mechanical characterization, metal forming, Ls-Dyna

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Authors: Abul B. M. M. K. Islam, Nuria Lopez-Bigas, Elizaveta V. Benevolenskaya

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RBP2 has shown to be important for cell differentiation control through epigenetic mechanism. The main aim of the present study is genome-wide location analysis of human RBP2 isoforms that differ in a histone-binding domain by ChIPseq. It is conceivable that the larger isoform (LI) of RBP2, which contains a specific H3K4me3 interacting domain, differs from the smaller isoform (SI) in genomic location, may account for the observed diversity in RBP2 function. To distinguish the two RBP2 isoforms, we used the fact that the SI lacks the C-terminal PHD domain and hence used the antibodies detecting both RBP2 isoforms (AI) through a common central domain, and the antibodies detecting only LI but not SI, through a C-terminal PHD domain. Overall our analysis suggests that RBP2 occupies about 77 nucleotides and binds GC rich motifs of active genes, does not bind to centromere, telomere, or enhancer regions, and binding sites are conserved compare to random. A striking difference between the only-SI and only-LI is that a large number of only-SI peaks are located in CpG islands and close to TSS compared to only-LI peaks. Enrichment analysis of the related genes indicates that several oncogenic pathways and metabolic pathways/processes are significantly enriched among only-SI/AI targets, but not LI/only-LI peak’s targets.

Keywords: bioinformatics, cancer, ChIP-seq, KDM5A

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Authors: Benjamin A. Ha, Marco Morselli, Xinhui Paige Zhang, Elizabeth A. C. Heath-Heckman, Jonathan B. Puritz, David K. Jacobs

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Next-generation sequencing has enhanced the ability to acquire massive amounts of sequence data to address classic population genetic questions for non-model organisms. Targeted approaches allow for cost effective or more precise analyses of relevant sequences; although, many such techniques require a known genome and it can be costly to purchase probes from a company. This is challenging for non-model organisms with no published genome and can be expensive for large population genetic studies. Expressed exome capture sequencing (EecSeq) synthesizes probes in the lab from expressed mRNA, which is used to capture and sequence the coding regions of genomic DNA from a pooled suite of samples. A normalization step produces probes to recover transcripts from a wide range of expression levels. This approach offers low cost recovery of a broad range of genes in the genome. This research project expands on EecSeq to investigate if mRNA from one taxon may be used to capture relevant sequences from a series of increasingly less closely related taxa. For this purpose, we propose to use the endangered Northern Tidewater goby, Eucyclogobius newberryi, a non-model organism that inhabits California coastal lagoons. mRNA will be extracted from E. newberryi to create probes and capture exomes from eight other taxa, including the more at-risk Southern Tidewater goby, E. kristinae, and more divergent species. Captured exomes will be sequenced, analyzed bioinformatically and phylogenetically, then compared to previously generated phylogenies across this group of gobies. This will provide an assessment of the utility of the technique in cross-species studies and for analyzing low genetic variation within species as is the case for E. kristinae. This method has potential applications to provide economical ways to expand population genetic and evolutionary biology studies for non-model organisms.

Keywords: coastal lagoons, endangered species, non-model organism, target capture method

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Authors: Kesavan Markkandan, Ha Young Park, Seung-Il Yoo, Sin-Gi Park, Junhyung Park

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For genetic identification of crop cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, PCR based, co-dominant and relatively abundant. However, new InDels need to be developed for genetic studies of new varieties due to the difference of allele frequencies in InDels among the population groups. These new varieties are evolved with low levels of genetic diversity in specific genome loci with high recombination rate. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a variation block (VB), where the genomes split by all assumed recombination sites. Firstly, VBs in crop cultivars were mined for transferability to VB-specific InDel markers. Secondly, putative InDels in the VB regions were identified for the development of barcode system by analyzing particular cultivar’s whole genome data. Thirdly, common VB-specific InDels from all cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the selected markers was assessed with other cultivars, and the barcode system that allows a clear distinction among those cultivars is described. The same approach can be applicable for other commercial crops. Hence, VB-based genetic identification not only minimize the molecular markers but also useful for assessing cultivars and for marker-assisted breeding in other crop species.

Keywords: variation block, polymorphism, InDel marker, genetic identification

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Authors: Juneseok You, Chanho Park, Kuehwan Jang, Sungsoo Na

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Sensing of nanotoxic materials is strongly important, as their engineering applications are growing recently and results in that nanotoxic material can harmfully influence human health and environment. In current study we report the quartz crystal microbalance (QCM)-based, in situ and real-time sensing of nanotoxic-material by frequency shift. We propose the in situ detection of nanotoxic material of zinc oxice by using QCM functionalized with a taget-specific DNA. Since the mass of a target material is comparable to that of an atom, the mass change caused by target binding to DNA on the quartz electrode is so small that it is practically difficult to detect the ions at low concentrations. In our study, we have demonstrated the in-situ and fast detection of zinc oxide using the quartz crystal microbalance (QCM). The detection was derived from the DNA hybridization between the DNA on the quartz electrode. The results suggest that QCM-based detection opens a new avenue for the development of a practical water-testing sensor.

Keywords: nanotoxic material, qcm, frequency, in situ sensing

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Authors: Herviyanti, Gusnidar, M. Harianti

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The objective of this research were: a) using low-rank coal (subbituminous) as main humate material sources because this material will not be anthracite, and cannot using to be an energy sources b) to examine residual effects of humic matter from subbituminous which was combined with P fertilizers to adsorp Al and Fe metal, improving soil fertility, and increasing P fertilizing efficiency and Oxisol productivity. Therefore, optimalization crop productivity of upland rice can be achieved. The experiment was designed using a 3 x 4 factorial with 3 replications in randomly groups design. The 1st factor was 3 ways incubating humate material with P-fertilizer, which are: I1 = Incubation of humate material 1 week, then incubation P-fertilizers 1 week; I2 = Incubation of humate materials and P fertilizers directly into the soil for 2 weeks; and I3 = humate material and P fertilizer mixed for 1 week, then incubation to the soil for 1 week. The 2nd factor was residual effects of humate material and P-fertilizer combination which are 4 doses H1 = 400 ppm (0.8 Mg/ha) + 100% R; H2 = 400 ppm + 75% R; H3 = 800 ppm (1.6 Mg/ha) + 100% R,; and H4 = 800 ppm + 75% R. The 2nd year research results showed that the best treatment was founded residue effect of 800 ppm humate material and 100% R P-fertilizer doses in I3 way incubation that is equal to 6.19 t ha-1 upland rice yield. However, this result is almost the same as residual effects of 800 ppm humate material + 75% R P-fertilizer doses and upland rice yield the 1st year. It was concluded that addition of humate material can given the efficiency of P-fertilizer using up to 25% until the 2nd season planted.

Keywords: humate materials, P-fertilizer, subbituminous, upland rice

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Authors: Hachmi Toifane, Pierre Tittelein, Anh Dung Tran Le, Laurent Zalewsi

Abstract:

This study introduces a composite material composed of bio-sourced phase-change material (PCM) of plant origin combined with hemp shives, developed in response to environmental challenges in the construction sector. The state of the art emphasizes the low thermal storage capacity of bio-based materials and highlights increasing need for developing sustainable materials that offer optimal thermal, mechanical, and hydric performances. The combining of PCM's thermal properties and hygric properties of hemp shives results in a material that combines lightness, strength, and hygrothermal regulation. Various formulations are being assessed and compared to conventional hemp concrete. Thermal characterization includes the measurements of thermal conductivity and numerical simulations to evaluate the thermal storage capacity. The results indicate that the addition of PCM significantly enhances the material's thermal storage capacity, positioning this one as a promising, eco-friendly solution for sustainable construction and for improving the energy efficiency of buildings.

Keywords: hemp composite, bio-sourced phase change material, thermal storage, hemp shives

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Authors: Samir Lecheb, Ahmed Chellil, Hamza Mechakra, Brahim Safi, Houcine Kebir

Abstract:

In this paper we studied fracture and dynamic behavior of vertical axis wind turbine blade, the VAWT is a historical machine, it has many properties, structure, advantage, component to be able to produce the electricity. We modeled the blade design then imported to Abaqus software for analysis the modes shapes, frequencies, stress, strain, displacement and stress intensity factor SIF, after comparison we chose the idol material. Finally, the CTS test of glass epoxy reinforced polymer plates to obtain the material fracture toughness Kc.

Keywords: blade, crack, frequency, material, SIF

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Authors: Tariq Bashir, Muhammad Waseem Tahir, Ulf Stigh, Behnaz Baghaie, Mikael Skrifvars

Abstract:

Absorption of moisture may cause many problems in a composite material, such as delamination, degradation of the strength and increase in the weight. For small coupons, the increase in weight may be negligible, however, for large structures increase in weight due to moisture absorption may be quite significant. Polyamides (PA6, PA66) absorb more moisture as compared to other thermoplastics. There are many parameters which affect the moisture absorption of the composite material for example temperature, pressure, type of matrix and fibers, thickness of the material and relative humidity (RH) etc. So, it is utmost important to investigate the impact of moisture on PA66 based composites which can be done by characterizing the mechanical properties of composite materials both for dry and wet conditions. In this study, laminates of C/PA66 composite are manufactured by first heating the commingled material in conventional oven at a temperature of 220 °C followed by pressing in a manual hot press for 20 minutes with preheated platen at 220 °C. To observe the moisture absorption of the composite, coupons of the material were placed in a climate chamber at five different conditions 0, 25, 50, 75 and 100% RH for 24 hours. Five specimens were used for each condition. These coupons were weighed before placing in the climate chamber and just after removing from the chamber to observe the moisture absorption of the material. The mechanical characterization such as tensile strength, flexural modulus, impact strength and DMTA of C/PA66 material are performed at 0, 50 and 100 % RH. The work is going on for the testing of the material and results will be presented in full paper.

Keywords: Carbon/Polyamide 66 composites, structural composites, mechanical characterizations, wet and dry conditions

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Authors: Jesha Faye T. Librea, Leslie Joy L. Diaz

Abstract:

Fuel-derived rice husk ash (fRHA) is a waste material from industries employing rice husk as a biomass fuel which, on the downside, causes disposal and environmental problems. To mitigate this, the fRHA was evaluated for use in other applications such as a pozzolanic material for the construction industry. In this study, the assessment of the potential of fRHA as pozzolanic supplementary cementitious material was conducted by determining the chemical and physical properties of fRHA according to ASTM C618, evaluating the fineness of the material according to ASTM C430, and determining its pozzolanic activity using Luxan Method. The material was found to have a high amorphous silica content of around 95.82 % with traces of alkaline and carbon impurities. The retained carbon residue is 7.18 %, which is within the limit of the specifications for natural pozzolans indicated in ASTM C618. The fineness of the fRHA is at 88.88 % retained at a 45-micron sieve, which, however, exceeded the limit of 34 %. This large particle size distribution was found to affect the pozzolanic activity of the fRHA. This was shown in the Luxan test, where the fRHA was identified as non-pozzolan due to its low pozzolanic activity index of 0.262. Thus, further processing must be done to the fRHA to pass the required ASTM fineness, have a higher pozzolanic activity index, and fully qualify as a pozzolanic material.

Keywords: rice husk ash, pozzolanic, fuel-derived ash, supplementary cementitious material

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Authors: Dhval Chauhan, Mahesh Chudasama

Abstract:

This study has been undertaken to give a review of Polyethylene Terephthalate Glycol (PETG) material used in Fused Deposition Modelling (FDM). This paper offers a review of the existing literature on polyethylene terephthalate glycol (PETG) material, the objective of the paper is to providing guidance on different process parameters that can be used to improve the strength of the part by performing various testing like tensile, compressive, flexural, etc. This work is target to find new paths that can be used for further development of the use of fiber reinforcement in PETG material.

Keywords: PETG, FDM, tensile strength, flexural strength, fiber reinforcement

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

Abstract:

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance

Procedia PDF Downloads 241

Authors: Soraya Hoornam, Zeinab Sanaee

Abstract:

Lithium-ion batteries are widely used for providing energy for mobile electronic devices. Graphite is a traditional anode material that was used in almost all commercialized lithium-ion batteries. It gives a specific capacity of 372 mAh/g for lithium storage. But there are multiple better choices for storing lithium that propose significantly higher specific capacities. As an example, silicon-based materials can be mentioned. In this regard, SiO₂ material can offer a huge specific capacity of 1965 mAh/g. Due to this high lithium storage ability, large volume change occurs in this electrode material during insertion and extraction of lithium, which may lead to cracking and destruction of the electrode. The use of nanomaterials instead of bulk material can significantly solve this problem. In addition, if we insert lithium in the active material of the battery before its cycling, which is called pre-lithiation, a further enhancement in the performance is expected. Here, we have fabricated an anode electrode of the battery using SiO₂ nanomaterial mixed with Graphite and assembled a lithium-ion battery half-cell with this electrode. Next, a pre-lithiation was performed on the SiO₂ nanoparticle-containing electrode, and the resulting anode material was investigated. This electrode has great potential for high-performance lithium-ion batteries.

Keywords: SiO₂ nanoparticles, lithium-ion battery, pre-lithiation, anode material

Procedia PDF Downloads 83