Search results for: simple sequence repeat markers

Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

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Authors: Sofia Sehli, Zainab El Ouafi, Casey Eddington, Soumaya Jbara, Kasambula Arthur Shem, Islam El Jaddaoui, Ayorinde Afolayan, Olaitan I. Awe, Allissa Dillman, Hassan Ghazal

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The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually.

Keywords: metagenomics, shotgun metagenomic sequence analysis, COVID-19, pipeline, bioinformatics

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Authors: Parul Johri, Mala Trivedi

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Major Intrinsic proteins (MIPs), actively involved in the passive transport of small polar molecules across the membranes of almost all living organisms. MIPs that specifically transport water molecules are named aquaporins (AQPs). The permeability of membranes is actively controlled by the regulation of the amount of different MIPs present but also in some cases by phosphorylation and dephosphorylation of the channel. Based on sequence similarity, MIPs have been classified into many categories. All of the proteins are made up of the 20 amino acids, the only difference is there in their orientations. Again all the 20 amino acids are made up of the basic five elements namely: carbon, hydrogen, oxygen, sulphur and nitrogen. These elements are responsible for giving the amino acids the properties of hydrophilicity/hydrophobicity which play an important role in protein interactions. The hydrophobic amino acids characteristically have greater number of carbon atoms as carbon is the main element which contributes to hydrophobic interactions in proteins. It is observed that the carbon level of proteins in different species is different. In the present work, we have taken a sample set of 150 aquaporins proteins from Uniprot database and a dynamic programming code was written to calculate the carbon percentage for each sequence. This carbon percentage was further used to barcode the aqauporins of animals and plants. The protein taken from Oryza sativa, Zea mays and Arabidopsis thaliana preferred to have carbon percentage of 31.8 to 35, whereas on the other hand sequences taken from Mus musculus, Saccharomyces cerevisiae, Homo sapiens, Bos Taurus, and Rattus norvegicus preferred to have carbon percentage of 31 to 33.7. This clearly demarks the carbon range in the aquaporin proteins from plant and animal origin. Hence the atom level analysis of protein sequences can provide us with better results as compared to the residue level comparison.

Keywords: aquaporins, carbon, dynamic prgramming, MIPs

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Authors: Sidra Pervez, Afsheen Aman, Shah Ali Ul Qader

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The importance of attaining an optimum performance of an enzyme is often a question of devising an effective method for its immobilization. Cross-linked enzyme aggregate (CLEAs) is a new approach for immobilization of enzymes using carrier free strategy. This method is exquisitely simple (involving precipitation of the enzyme from aqueous buffer followed by cross-linking of the resulting physical aggregates of enzyme molecules) and amenable to rapid optimization. Among many industrial enzymes, amyloglucosidase is an important amylolytic enzyme that hydrolyzes alpha (1→4) and alpha (1→6) glycosidic bonds in starch molecule and produce glucose as a sole end product. Glucose liberated by amyloglucosidase can be used for the production of ethanol and glucose syrups. Besides this amyloglucosidase can be widely used in various food and pharmaceuticals industries. For production of amyloglucosidase on commercial scale, filamentous fungi of genera Aspergillus are mostly used because they secrete large amount of enzymes extracellularly. The current investigation was based on isolation and identification of filamentous fungi from genus Aspergillus for the production of amyloglucosidase in submerged fermentation and optimization of cultivation parameters for starch saccharification. Natural isolates were identified as Aspergillus niger KIBGE-IB36, Aspergillus fumigatus KIBGE-IB33, Aspergillus flavus KIBGE-IB34 and Aspergillus terreus KIBGE-IB35 on taxonomical basis and 18S rDNA analysis and their sequence were submitted to GenBank. Among them, Aspergillus fumigatus KIBGE-IB33 was selected on the basis of maximum enzyme production. After optimization of fermentation conditions enzyme was immobilized on CLEA. Different parameters were optimized for maximum immobilization of amyloglucosidase. Data of enzyme stability (thermal and Storage) and reusability suggested the applicability of immobilized amyloglucosidase for continuous saccharification of starch in industrial processes.

Keywords: aspergillus, immobilization, industrial processes, starch saccharification

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Authors: Ahmed Hamida Boudinar, Noureddine Benouzza, Azeddine Bendiabdellah, Mohamed El Amine Khodja

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This paper describes a new diagnosis approach for identification of the progressive stator winding inter-turn short-circuit fault in induction motor. This approach is based on a simple monitoring of the combined information related to both magnitude and phase-angle obtained from the fundamental by the three line currents frequency analysis. In addition, to simplify the interpretation and analysis of the data; a new graphical tool based on a triangular representation is suggested. This representation, depending on its size, enables to visualize in a simple and clear manner, the existence of the stator inter-turn short-circuit fault and its discrimination with respect to a healthy stator. Experimental results show well the benefit and effectiveness of the proposed approach.

Keywords: induction motor, magnitude, phase-angle, spectral analysis, stator fault

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Authors: Vikram Singh

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The objective of the study was to study the effectiveness of common yoga protocol on reaction time (simple visual reaction time-SVRT measured in milliseconds/seconds) of male football players in the age group of 15 to 21 years. The 40 boys were randomly assigned into two groups i.e. control and experimental. SVRT for both the groups were measured on day-1 and post intervention (common yoga protocol here) was measured after 45 days of training to the experimental group only. One way ANOVA (Univariate analysis) and Independent t-test using SPSS 23 statistical package was applied to get and analyze the results. There was a significant difference after 45 days of yoga protocol in simple visual reaction time of experimental group (p = .032), t (33.05) = 3.881, p = .000 (two-tailed). Null hypothesis (that there would be no post measurement differences in reaction times of control and experimental groups) was rejected. Where p<.05. Therefore alternate hypothesis was accepted.

Keywords: footballers, t-test, yoga protocol, reaction time

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Authors: Isaac K. E. Ampomah, Seong-Bae Park, Sang-Jo Lee

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Over the past decade, there have been promising developments in Natural Language Processing (NLP) with several investigations of approaches focusing on Recognizing Textual Entailment (RTE). These models include models based on lexical similarities, models based on formal reasoning, and most recently deep neural models. In this paper, we present a sentence encoding model that exploits the sentence-to-sentence relation information for RTE. In terms of sentence modeling, Convolutional neural network (CNN) and recurrent neural networks (RNNs) adopt different approaches. RNNs are known to be well suited for sequence modeling, whilst CNN is suited for the extraction of n-gram features through the filters and can learn ranges of relations via the pooling mechanism. We combine the strength of RNN and CNN as stated above to present a unified model for the RTE task. Our model basically combines relation vectors computed from the phrasal representation of each sentence and final encoded sentence representations. Firstly, we pass each sentence through a convolutional layer to extract a sequence of higher-level phrase representation for each sentence from which the first relation vector is computed. Secondly, the phrasal representation of each sentence from the convolutional layer is fed into a Bidirectional Long Short Term Memory (Bi-LSTM) to obtain the final sentence representations from which a second relation vector is computed. The relations vectors are combined and then used in then used in the same fashion as attention mechanism over the Bi-LSTM outputs to yield the final sentence representations for the classification. Experiment on the Stanford Natural Language Inference (SNLI) corpus suggests that this is a promising technique for RTE.

Keywords: deep neural models, natural language inference, recognizing textual entailment (RTE), sentence-to-sentence relation

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Authors: Svetlana Guryeva, Inna Kornienko, Andrey Usanov, Dmitry Usanov, Elena Petersen

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Every day cells in our organism are exposed to various factors: chemical agents, reactive oxygen species, ionizing radiation, and others. These factors can cause damage to DNA, cellular membrane, intracellular compartments, and proteins. The fate of cells depends on the exposure intensity and duration. The prolonged and intense exposure causes the irreversible damage accumulation, which triggers the permanent cell cycle arrest (cellular senescence) or cell death programs. In the case of low dose of impacts, it can lead to cell renovation and to cell functional state improvement. Therefore, it is a pivotal question to investigate the factors and doses that result in described positive effects. In order to estimate the influence of different agents, the proliferation index and levels of cell death markers (annexin V/propidium iodide), senescence-associated β-galactosidase, and lipofuscin were measured. The experiments were conducted on primary human fibroblasts of the 8th passage. According to the levels of mentioned markers, these cells were defined as senescent cells. The effect of low-frequency magnetic field was investigated. Different modes of magnetic field exposure were tested. The physical agents were compared with chemical agents: metformin (10 mM) and taurine (0.8 mM and 1.6 mM). Cells were incubating with chemicals for 5 days. The highest decrease in the level of senescence-associated β-galactosidase (21%) and lipofuscin (17%) was observed in the primary senescent fibroblasts after 5 days after double treatments with 48 h intervals with low-frequency magnetic field. There were no significant changes in the proliferation index after magnetic field application. The cytotoxic effect of magnetic field was not observed. The chemical agent taurine (1.6 mM) decreased the level of senescence-associated β-galactosidase (23%) and lipofuscin (22%). Metformin improved the activity of senescence-associated β-galactosidase on 15% and the level of lipofuscin on 19% in this experiment. According to these results, the effect of double treatment with 48 h interval with low-frequency magnetic field and the effect of taurine (1.6 mM) were comparable to the effect of metformin, for which anti-aging properties are proved. In conclusion, this study can become the first step towards creation of the standardized system for the investigation of different effects on senescent cells.

Keywords: biomarkers, magnetic field, metformin, primary fibroblasts, senescence, taurine

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Authors: Randa Boukhris, Alima Damak, Dorra Sellami

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Fingervein biometric authentication is one of the most popular and accurate technologies. However, low cost embedded solution is still an open problem. In this paper, a real-time implementation of fingervein recognition process embedded in Raspberry-Pi has been proposed. The use of Raspberry-Pi reduces overall system cost and size while allowing an easy user interface. Implementation of a target technology has guided to opt some specific parallel and simple processing algorithms. In the proposed system, we use four structural directional kernel elements for filtering finger vein images. Then, a Top-Hat and Bottom-Hat kernel filters are used to enhance the visibility and the appearance of venous images. For feature extraction step, a simple Local Directional Code (LDC) descriptor is applied. The proposed system presents an Error Equal Rate (EER) and Identification Rate (IR), respectively, equal to 0.02 and 98%. Furthermore, experimental results show that real-time operations have good performance.

Keywords: biometric, Bottom-Hat, Fingervein, LDC, Rasberry-Pi, ROI, Top-Hat

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Authors: Glaoui Hachemi

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In this paper, a scheme based on multi-input multi output Fuzzy Sliding Mode control (MIMO-FSMC) for linear speed regulation of winding system is proposed. Once the uncoupled model of the winding system was obtained, a smooth control function with a threshold was selected to indicate how far away the case was from the sliding surface. nevertheless, this control function depends closely on the higher bound of the uncertainties, which generates overlap. So, this size has to be chosen with broad care to obtain high performances. Usually, the upper bound of uncertainties is difficult to know before motor operation, so, a Fuzzy Sliding Mode controller is investigated to resolve this problem, a simple Fuzzy inference mechanism is used to decrease the chattering phenomenon by simple adjustments. A simulation study is achieved and that the indicate fuzzy sliding mode controllers have great potential for use as an alternative to the conventional sliding mode control.

Keywords: Winding system, induction machine, Mechanical tension, Proportional-integral (PI), sliding mode control, Fuzzy logic

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Authors: Nkwanyang L. Takem, Christopher M. Agyingi

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Background and aim: An integrated interpretation of wireline logs and lithology of two selected wells (KF-1 and KF-2) of Kribi oil field within the southeastern offshore Douala/Kribi Campo Basin was carried out for sequence stratigraphic analysis of sediments penetrated by the wells. Methods: The stratigraphic units within the wells were subdivided into depositional sequences using characteristic well log patterns that were deposited between Tertiary Miocene to lower Cretaceous. Results: Nine (9) and eight (8) depositional sequences were identified respectively for KF-1 and KF-2. The sequences comprise LST (progradational packages), TSTs (retrogradational packages) and HSTs (aggradational packages), which reflect depositional systems deposited during different phases of base-level changes. The (LST) consists of Basin Floor Fans (BFF), Slope Fans and Channel Sands deposited when sea level was low and accommodation space lower than rate of sediment influx. TST consists of retrogradational marine shales deposited during high relative sea levels and when accommodation space was higher than rate of sediment influx. HST consisted of shoreface sands displaying mostly aggradational to progradational stacking patterns. Conclusion: The rapid facies changes between successive systems tracts provide potential stratigraphic traps. Reservoir stratification and continuity vary greatly between systems tracts and this enhanced development of stratigraphic traps in the area. Basin floor fans comprise sandstone of good reservoir quality, thus huge accumulation of HC can be trapped in this reservoirs.

Keywords: Douala-Kribi-Campo Basin, reservoirs, sequence strastigraphyy, system tracks

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Authors: Jannis Kountouras, Nikolaos Kapetanakis, Stergios A. Polyzos, Apostolis Papaeftymiou, Panagiotis Katsinelos, Ioannis Venizelos, Christina Nikolaidou, Christos Zavos, Iordanis Romiopoulos, Elena Tsiaousi, Evangelos Kazakos, Michael Doulberis

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Background & Aims: Helicobacter pylori infection (Hp-I) has been recognized as a substantial risk agent involved in gastrointestinal (GI) tract oncogenesis by stimulating cancer stem cells (CSCs), oncogenes, immune surveillance processes, and triggering GI microbiota dysbiosis. We aimed to investigate the possible involvement of active Hp-I in the sequence: chronic inflammation–adenoma–colorectal cancer (CRC) development. Methods: Four pillars were investigated: (i) endoscopic and conventional histological examinations of patients with CRC, colorectal adenomas (CRA) versus controls to detect the presence of active Hp-I; (ii) immunohistochemical determination of the presence of Hp; expression of CD44, an indicator of CSCs and/or bone marrow-derived stem cells (BMDSCs); expressions of oncogene Ki67 and anti-apoptotic Bcl-2 protein; (iii) expression of CD45, indicator of immune surveillance locally (assessing mainly T and B lymphocytes locally); and (iv) correlation of the studied parameters with the presence or absence of Hp-I. Results: Among 50 patients with CRC, 25 with CRA, and 10 controls, a significantly higher presence of Hp-I in the CRA (68%) and CRC group (84%) were found compared with controls (30%). The presence of Hp-I with accompanying immunohistochemical expression of CD44 in biopsy specimens was revealed in a high proportion of patients with CRA associated with moderate/severe dysplasia (88%) and CRC patients with moderate/severe degree of malignancy (91%). Comparable results were also obtained for Ki67, Bcl-2, and CD45 immunohistochemical expressions. Concluding Remarks: Hp-I seems to be involved in the sequence: CRA – dysplasia – CRC, similarly to the upper GI tract oncogenesis, by several pathways such as the following: Beyond Hp-I associated insulin resistance, the major underlying mechanism responsible for the metabolic syndrome (MetS) that increase the risk of colorectal neoplasms, as implied by other Hp-I related MetS pathologies, such as non-alcoholic fatty liver disease and upper GI cancer, the disturbance of the normal GI microbiota (i.e., dysbiosis) and the formation of an irritative biofilm could contribute to a perpetual inflammatory upper GIT and colon mucosal damage, stimulating CSCs or recruiting BMDSCs and affecting oncogenes and immune surveillance processes. Further large-scale relative studies with a pathophysiological perspective are necessary to demonstrate in-depth this relationship.

Keywords: Helicobacter pylori, colorectal cancer, colorectal adenomas, gastrointestinal oncogenesis

Procedia PDF Downloads 146

Authors: Rijnbout-St.James Willem, Lindner Volkhard, Scholand Mary Beth, Ashton M. Tillett, Di Gennaro Michael Jude, Smith Silvia Enrica

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Introduction: Fibrosing lung diseases are characterized by changes in the lung interstitium and are classified based on etiology: 1) environmental/exposure-related, 2) autoimmune-related, 3) sarcoidosis, 4) interstitial pneumonia, and 4) idiopathic. Among interstitial lung diseases (ILD) idiopathic forms, idiopathic pulmonary fibrosis (IPF) is the most severe. Pathogenesis of IPF is characterized by an increased presence of proinflammatory mediators, resulting in alveolar injury, where injury to alveolar epithelium precipitates an increase in collagen deposition, subsequently thickening the alveolar septum and decreasing gas exchange. Identifying biomarkers implicated in the pathogenesis of lung fibrosis is key to developing new therapies and improving the efficacy of existing therapies. The transforming growth factor-beta (TGF-B1), a mediator of tissue repair associated with WNT5A signaling, is partially responsible for fibroblast proliferation in ILD and is the target of Pirfenidone, one of the antifibrotic therapies used for patients with IPF. Canonical TGF-B signaling is mediated by the proteins SMAD 2/3, which are, in turn, indirectly regulated by Collagen Triple Helix Repeat Containing 1 (CTHRC1). In this study, we tested the following hypotheses: 1) CTHRC1 is more elevated in the ILD cohort compared to unaffected controls, and 2) CTHRC1 is differently expressed among ILD types. Material and Methods: CTHRC1 levels were measured by ELISA in 171 plasma samples from the deidentified University of Utah ILD cohort. Data represent a cohort of 131 ILD-affected participants and 40 unaffected controls. CTHRC1 samples were categorized by a pulmonologist based on affectation status and disease subtypes: IPF (n = 45), sarcoidosis (4), nonspecific interstitial pneumonia (16), hypersensitivity pneumonitis (n = 7), interstitial pneumonia (n=13), autoimmune (n = 15), other ILD - a category that includes undifferentiated ILD diagnoses (n = 31), and unaffected controls (n = 40). We conducted a single-factor ANOVA of plasma CTHRC1 levels to test whether CTHRC1 variance among affected and non-affected participants is statistically significantly different. In-silico analysis was performed with Ingenuity Pathway Analysis® to characterize the role of CTHRC1 in the pathway of lung fibrosis. Results: Statistical analyses of CTHRC1 in plasma samples indicate that the average CTHRC1 level is significantly higher in ILD-affected participants than controls, with the autoimmune ILD being higher than other ILD types, thus supporting our hypotheses. In-silico analyses show that CTHRC1 indirectly activates and phosphorylates SMAD3, which in turn cross-regulates TGF-B1. CTHRC1 also may regulate the expression and transcription of TGFB-1 via WNT5A and its regulatory relationship with CTNNB1. Conclusion: In-silico pathway analyses demonstrate that CTHRC1 may be an important biomarker in ILD. Analysis of plasma samples indicates that CTHRC1 expression is positively associated with ILD affectation, with autoimmune ILD having the highest average CTHRC1 values. While characterizing CTHRC1 levels in plasma can help to differentiate among ILD types and predict response to Pirfenidone, the extent to which plasma CTHRC1 level is a function of ILD severity or chronicity is unknown.

Keywords: interstitial lung disease, CTHRC1, idiopathic pulmonary fibrosis, pathway analyses

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Authors: Arash Jafari, Mehdi Taghaddosi, Azin Parvin

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In the paper, our purpose is to enhance the ability to solve a nonlinear differential equation which is about the motion of an incompressible fluid flow going down of an inclined plane without thermal effect with a simple and innovative approach which we have named it new method. Comparisons are made amongst the Numerical, new method, and HPM methods, and the results reveal that this method is very effective and simple and can be applied to other nonlinear problems. It is noteworthy that there are some valuable advantages in this way of solving differential equations, and also most of the sets of differential equations can be answered in this manner which in the other methods they do not have acceptable solutions up to now. A summary of the excellence of this method in comparison to the other manners is as follows: 1) Differential equations are directly solvable by this method. 2) Without any dimensionless procedure, we can solve equation(s). 3) It is not necessary to convert variables into new ones. According to the afore-mentioned assertions which will be proved in this case study, the process of solving nonlinear equation(s) will be very easy and convenient in comparison to the other methods.

Keywords: viscos fluid, incompressible fluid flow, inclined plane, nonlinear phenomena

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Authors: Shazi Farooqui, Anupam Sharma

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The Mahi River (~600km long) is an important west flowing the river of Central India. It originates in Madhya Pradesh and starts flowing in NW direction and enters into the state of Rajasthan. It flows across southern Rajasthan and then enters into Gujarat and finally debouches in the Gulf of Cambay. In Gujarat state, it flows through all four geomorphic zones i.e. eastern upland zone, shallow buried piedmont zone, alluvial zone and coastal zone. In lower reaches and particularly when it is flowing under the coastal regime, it provides an opportunity to study – 1. Land–Sea interaction and role of relative sea level changes, 2. Coastal/estuarine geological process, 3. Landscape evolution in marginal areas and so on. The Late Quaternary deposits of Mainland Gujarat is appreciably studied by Chamyal and his group of MS University of Baroda, and they have established that the 30-35m thick sediment package of the Mainland Gujarat is comprised of marine, fluvial and aeolian sediments. It is also established that in the estuarine zone, the upper few meter thick sediments package is of marine nature. However, its thickness, characters and the depositional environment including the role of climate and tectonics is still not clearly defined. To understand few aspects of the above mentioned, in the present study, a 17m subsurface sediment core has been retrieved from the estuarine zone of Mahi river basin. The Multiproxy studies which include the textural analysis (grain size), Loss on ignition (LOI), Bulk and clay mineralogy and geochemical studies have been carried out. In the entire sedimentary sequence, the grain size largely varies from coarse sand to clay; however, a solitary gravel bed is also noticed. The lower part (depth 9-17m), is mainly comprised of sub equal proportion of sand and silt. The sediments mainly have bimodal and leptokurtic distribution and deposited in alternate sand-silt package, probably indicating flood deposits. Relatively low moisture (1.8%) and organic carbon (2.4%) with increased carbonate values (12%) indicate that conditions must have to remain oxidizing. The middle part (depth 9–6m) has a 1m thick gravel bed at the bottom and overlain by coarse sand to very fine sand showing fining upward sequence. The presence of gravel bed suggests some kind of tectonic activity resulting into change in base level or enhanced precipitation in the catchment region. The upper part (depth 6–0m; top part of sequence) mainly comprised of fine sand to silt size grains (with appreciable clay content). The sediment of this part is Unimodal and very leptokurtic in nature suggesting wave and winnowing process and deposited in low energy suspension environment. This part has relatively high moisture (2.1%) and organic carbon (2.7%) with decreased carbonate content (4.2%) indicating change in the depositional environment probably under estuarine conditions. The presence of chlorite along with smectite clay mineral further supports the significant marine contribution in the formation of upper part of the sequence.

Keywords: grain size, statistical analysis, clay minerals, late quaternary, LOI

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Authors: Monika Chuchro

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This paper presents a preliminary attempt to apply classification of time series using meta-clusters in order to improve the quality of regression models. In this case, clustering was performed as a method to obtain a subgroups of time series data with normal distribution from inflow into waste water treatment plant data which Composed of several groups differing by mean value. Two simple algorithms: K-mean and EM were chosen as a clustering method. The rand index was used to measure the similarity. After simple meta-clustering, regression model was performed for each subgroups. The final model was a sum of subgroups models. The quality of obtained model was compared with the regression model made using the same explanatory variables but with no clustering of data. Results were compared by determination coefficient (R2), measure of prediction accuracy mean absolute percentage error (MAPE) and comparison on linear chart. Preliminary results allows to foresee the potential of the presented technique.

Keywords: clustering, data analysis, data mining, predictive models

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Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: Adandé Belarmain Fandohan

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Climate change has become a major concern globally, particularly in rural communities that have to find rapid coping solutions. Several vulnerability assessment approaches have been developed in the last decades. This comes along with a higher risk for different methods to result in different conclusions, thereby making comparisons difficult and decision-making non-consistent across areas. The effect of methods and computational approaches on estimates of people’s vulnerability was assessed using data collected from the Gambia. Twenty-four indicators reflecting vulnerability components: (exposure, sensitivity, and adaptive capacity) were selected for this purpose. Data were collected through household surveys and key informant interviews. One hundred and fifteen respondents were surveyed across six communities and two administrative districts. Results were compared over three computational approaches: the maximum value transformation normalization, the z-score transformation normalization, and simple averaging. Regardless of the approaches used, communities that have high exposure to climate change and extreme events were the most vulnerable. Furthermore, the vulnerability was strongly related to the socio-economic characteristics of farmers. The survey evidenced variability in vulnerability among communities and administrative districts. Comparing output across approaches, overall, people in the study area were found to be highly vulnerable using the simple average and maximum value transformation, whereas they were only moderately vulnerable using the z-score transformation approach. It is suggested that assessment approach-induced discrepancies be accounted for in international debates to harmonize/standardize assessment approaches to the end of making outputs comparable across regions. This will also likely increase the relevance of decision-making for adaptation policies.

Keywords: maximum value transformation, simple averaging, vulnerability assessment, West Africa, z-score transformation

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Authors: S. Koppikar, P. Kulkarni, D. Ingale , N. Wagh, S. Deshpande, A. Mahajan, A. Harsulkar

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Crucial role of reactive oxygen species (ROS) in the progression Osteoarthritis (OA) pathogenesis has been endorsed several times though its exact mechanism remains unclear. Oxidative stress is known to instigate classical stress factors such as cytokines, chemokines and ROS, which hampers cartilage remodelling process and ultimately results in worsening the disease. Synovial fluid (SF) is a biological communicator between cartilage and synovium that accumulates redox and biochemical signalling mediators. The present work attempts to measure several oxidative stress markers in the synovial fluid obtained from knee OA patients with varying degree of disease severity. Thirty OA and five Meniscal-tear (MT) patients were graded using Kellgren-Lawrence scale and assessed for Nitric oxide (NO), Nitrate-Nitrite (NN), 2,2-diphenyl-1-picrylhydrazyl (DPPH), Ferric Reducing Antioxidant Potential (FRAP), Catalase (CAT), Superoxide dismutase (SOD) and Malondialdehyde (MDA) levels for comparison. Out of various oxidative markers studied, NO and SOD showed significant difference between moderate and severe OA (p= 0.007 and p= 0.08, respectively), whereas CAT demonstrated significant difference between MT and mild group (p= 0.07). Interestingly, NN revealed statistically positive correlation with OA severity (p= 0.001 and p= 0.003). MDA, a lipid peroxidation by-product was estimated maximum in early OA when compared to MT (p= 0.06). However, FRAP did not show any correlation with OA severity or MT control. NO is an essential bio-regulatory molecule essential for several physiological processes, and inflammatory conditions. However, due to its short life, exact estimation of NO becomes difficult. NO and its measurable stable products are still it is considered as one of the important biomarker of oxidative damage. Levels of NO and nitrite-nitrate in SF of patients with OA indicated its involvement in the disease progression. When SF groups were compared, a significant correlation among moderate, mild and MT groups was established. To summarize, present data illustrated higher levels of NO, SOD, CAT, DPPH and MDA in early OA in comparison with MT, as a control group. NN had emerged as a prognostic bio marker in knee OA patients, which may act as futuristic targets in OA treatment.

Keywords: antioxidant, knee osteoarthritis, oxidative stress, synovial fluid

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Authors: O. I. H. Dimitry, N. A. Mansour, A. L. G. Saad

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Natural sodium montmorillonite (NaMMT), Cloisite Na⁺ and two organophilic montmorillonites (OMMTs), Cloisites 20A and 15A were used. Polycaprolactone (PCL)/MMT composites containing 1, 3, 5, and 10 wt% of Cloisite Na⁺ and PCL/OMMT nanocomposites containing 5 and 10 wt% of Cloisites 20A and 15A were prepared via solution intercalation technique to study the influence of organic modifier loading on particle dispersion of PCL/ NaMMT composites. Thermal stabilities of the obtained composites were characterized by thermal analysis using the thermogravimetric analyzer (TGA) which showed that in the presence of nitrogen flow the incorporation of 5 and 10 wt% of filler brings some decrease in PCL thermal stability in the sequence: Cloisite Na+>Cloisite 15A > Cloisite 20A, while in the presence of air flow these fillers scarcely influenced the thermoxidative stability of PCL by slightly accelerating the process. The interaction between PCL and silicate layers was studied by Fourier transform infrared (FTIR) spectroscopy which confirmed moderate interactions between nanometric silicate layers and PCL segments. The electrical conductivity (σ) which describes the ionic mobility of the systems was studied as a function of temperature and showed that σ of PCL was enhanced on increasing the modifier loading at filler content of 5 wt%, especially at higher temperatures in the sequence: Cloisite Na⁺<Cloisite 20A<Cloisite 15A, and was then decreased to some extent with a further increase to 10 wt%. The activation energy E_σ obtained from the dependency of σ on temperature using Arrhenius equation was found to be lowest for the nanocomposite containing 5 wt% of Cloisite 15A. The dispersed behavior of clay in PCL matrix was evaluated by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses which revealed partial intercalated structures in PCL/NaMMT composites and semi-intercalated/semi-exfoliated structures in PCL/OMMT nanocomposites containing 5 wt% of Cloisite 20A or Cloisite 15A.

Keywords: electrical conductivity, montmorillonite, nanocomposite, organoclay, polycaprolactone

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Authors: N. Beit Saeid

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Cyclones are used in the field of air industrial gases pollution and control the pollution with centrifugal forces that is generated with spatial geometry of the cyclone. Their simple design, low capital and maintenance costs and adaptability to a wide range of operating conditions have made cyclones one of the most widely used industrial dust collectors. Their cost of operation is proportional to the fan energy required to overcome their pressure drop. Optimized geometry of outlet diffuser of the cyclones potentially could reduce exit pressure losses without affecting collection efficiency. Three rectangular outlets and a radial outlet with a variable opening had been analyzed on two cyclones. Pressure drop was investigated for inlet velocities from about 10 to 20 m s−1. The radial outlet reduced cyclone pressure drop by between 8.7 and 11.9 percent when its exit area was equal to the flow area of the cyclone vortex finder or gas exit. A simple payback based on avoided energy costs was estimated to be between 3600 and 5000 h, not including installation cost.

Keywords: cyclone, CFD, optimization, genetic algorithm

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Authors: Mohammed A. Sakr, Tarek M. Khalifa, Walid N. Mansour

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Fiber reinforced polymer (FRP) installation is a very effective way to repair and strengthen structures that have become structurally weak over their life span. This technique attracted the concerning of researchers during the last two decades. This paper presents a simple uniaxial nonlinear finite element model (UNFEM) able to accurately estimate the load-carrying capacity, different failure modes and the interfacial stresses of reinforced concrete (RC) continuous beams flexurally strengthened with externally bonded FRP plates on the upper and lower fibers. Results of the proposed finite element (FE) model are verified by comparing them with experimental measurements available in the literature. The agreement between numerical and experimental results is very good. Considering fracture energy of adhesive is necessary to get a realistic load carrying capacity of continuous RC beams strengthened with FRP. This simple UNFEM is able to help design engineers to model their strengthened structures and solve their problems.

Keywords: continuous beams, debonding, finite element, fibre reinforced polymer

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Authors: Mohammad Shams Esfand Abadi, Mehrdad Zalaghi, Reza ebrahimpour

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In this paper, we propose a sign adaptive filter algorithm with the ability of dynamic selection of subband filters which leads to low computational complexity compared with conventional sign subband adaptive filter (SSAF) algorithm. Dynamic selection criterion is based on largest reduction of the mean square deviation at each adaption. We demonstrate that this simple proposed algorithm has the same performance of the conventional SSAF and somewhat faster than it. In the presence of impulsive interferences robustness of the simple proposed algorithm as well as the conventional SSAF and outperform the conventional normalized subband adaptive filter (NSAF) algorithm. Therefore, it is preferred for environments under impulsive interferences. Simulation results are presented to verify these above considerations very well have been achieved.

Keywords: acoustic echo cancellation (AEC), normalized subband adaptive filter (NSAF), dynamic selection subband adaptive filter (DS-NSAF), sign subband adaptive filter (SSAF), impulsive noise, robust filtering

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Authors: Hyeon-Kyo Lim, Hyunjung Kim, Kune-Woo Lee

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Decommissioning process of nuclear facilities can be said to consist of a sequence of problem solving activities, partly because there may exist working environments contaminated by radiological exposure, and partly because there may also exist industrial hazards such as fire, explosions, toxic materials, and electrical and physical hazards. As for an individual hazard factor, risk assessment techniques are getting known to industrial workers with advance of safety technology, but the way how to integrate those results is not. Furthermore, there are few workers who experienced decommissioning operations a lot in the past. Therefore, not a few countries in the world have been trying to develop appropriate counter techniques in order to guarantee safety and efficiency of the process. In spite of that, there still exists neither domestic nor international standard since nuclear facilities are too diverse and unique. In the consequence, it is quite inevitable to imagine and assess the whole risk in the situation anticipated one by one. This paper aimed to find out an appropriate technique to integrate individual risk assessment results from the viewpoint of experts. Thus, on one hand the whole risk assessment activity for decommissioning operations was modeled as a sequence of individual risk assessment steps, and on the other, a hierarchical risk structure was developed. Then, risk assessment procedure that can elicit individual hazard factors one by one were introduced with reference to the standard operation procedure (SOP) and hierarchical task analysis (HTA). With an assumption of quantification and normalization of individual risks, a technique to estimate relative weight factors was tried by using the conventional Analytic Hierarchical Process (AHP) and its result was reviewed with reference to judgment of experts. Besides, taking the ambiguity of human judgment into consideration, debates based upon fuzzy inference was added with a mathematical case study.

Keywords: decommissioning, risk assessment, analytic hierarchical process (AHP), fuzzy inference

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Authors: Stuart Bradley, Mathew Legg, Lilyan Panton

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Ultrasonic remote sensing is a useful tool for assessing the interior structure of complex targets. For these methods, significantly enhanced spatial resolution is obtained if the pulse is coded, for example using a linearly changing frequency during the pulse duration. Such pulses have a time-dependent spectral structure. Interpretation of the backscatter from targets is, therefore, complicated if the scattering is frequency-dependent. While analytic models are well established for steady sinusoidal excitations applied to simple shapes such as spheres, such models do not generally exist for temporally evolving excitations. Therefore, models are developed in the current paper for handling such signals so that the properties of the targets can be quantitatively evaluated while maintaining very high spatial resolution. Laboratory measurements on simple shapes are used to confirm the validity of the models.

Keywords: linear FM chirp, time-dependent acoustic scattering, ultrasonic remote sensing, ultrasonic scattering

Procedia PDF Downloads 317

Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Rajkumar Ghosh

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The paper presents a comprehensive study of the structural analysis of the Chaura Thrust in Himachal Pradesh, India. The research focuses on several key aspects, including the activation timing of the Main Central Thrust (MCT) and the South Tibetan Detachment System (STDS), the identification and characterization of mylonitised zones through microscopic examination, and the understanding of box fold characteristics and their implications in the regional geology of the Himachal Himalaya. The primary objective of the study is to provide field documentation of the Chaura Thrust, which was previously considered a blind thrust with limited field evidence. Additionally, the research aims to characterize box folds and their signatures within the broader geological context of the Himachal Himalaya, document the temperature range associated with grain boundary migration (GBM), and explore the overprinting structures related to multiple sets of Higher Himalayan Out-of-Sequence Thrusts (OOSTs). The research methodology employed geological field observations and microscopic studies. Samples were collected along the Jhakri-Chaura transect at regular intervals of approximately 1 km to conduct strain analysis. Microstructural studies at the grain scale along the Jhakri-Wangtu transect were used to document the GBM-associated temperature range. The study reveals that the MCT activated in two parts, as did the STDS, and provides insights into the activation ages of the Main Boundary Thrust (MBT) and the Main Frontal Thrust (MFT). Under microscopic examination, the study identifies two mylonitised zones characterized by S-C fabric, and it documents dynamic and bulging recrystallization, as well as sub-grain formation. Various types of crenulated schistosity are observed in photomicrographs, including a rare occurrence where crenulation cleavage and sigmoid Muscovite are found juxtaposed. The study also notes the presence of S/SE-verging meso- and micro-scale box folds around Chaura, which may indicate structural upliftment. Kink folds near Chaura are visible, while asymmetric shear sense indicators in augen mylonite are predominantly observed under microscopic examination. Moreover, the research highlights the documentation of the Higher Himalayan Out-of-Sequence Thrust (OOST) in Himachal Pradesh, which activated the MCT and occurred within a zone south of the Main Central Thrust Upper (MCTU). The presence of multiple sets of OOSTs suggests a zigzag pattern of strain accumulation in the area. The study emphasizes the significance of understanding the overprinting structures associated with OOSTs. Overall, this study contributes to the understanding of the structural analysis of the Chaura Thrust and its implications in the regional geology of the Himachal Himalaya. The research underscores the importance of microscopic studies in identifying mylonitised zones and various types of crenulated schistosity. Additionally, the study documents the GBM-associated temperature range and provides insights into the activation of the Higher Himalayan Out-of-Sequence Thrust (OOST) in Himachal Pradesh. The findings of the study were obtained through geological field observations, microscopic studies, and strain analysis, offering valuable insights into the activation timing, mylonitization characteristics, and overprinting structures related to the Chaura Thrust and the broader tectonic framework of the region.

Keywords: Main Central Thrust, Jhakri Thrust, Chaura Thrust, Higher Himalaya, Out-of-Sequence Thrust, Sarahan Thrust

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Authors: Abu Salim Mustafa

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Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: mycobacterium tuberculosis, PPE68, peptides, vaccine

Procedia PDF Downloads 137

Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

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Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs

Procedia PDF Downloads 246

Authors: Arun Goel

Abstract:

Prediction of maximum local scour is necessary for the safety and economical design of the bridges. A number of equations have been developed over the years to predict local scour depth using laboratory data and a few pier equations have also been proposed using field data. Most of these equations are empirical in nature as indicated by the past publications. In this paper, attempts have been made to compute local depth of scour around bridge pier in dimensional and non-dimensional form by using linear regression, simple regression and SVM (Poly and Rbf) techniques along with few conventional empirical equations. The outcome of this study suggests that the SVM (Poly and Rbf) based modeling can be employed as an alternate to linear regression, simple regression and the conventional empirical equations in predicting scour depth of bridge piers. The results of present study on the basis of non-dimensional form of bridge pier scour indicates the improvement in the performance of SVM (Poly and Rbf) in comparison to dimensional form of scour.

Keywords: modeling, pier scour, regression, prediction, SVM (Poly and Rbf kernels)

Procedia PDF Downloads 452