Search results for: pipeline inspection

Authors: Atul Khurana, Rajul Rastogi, Hans-Joachim Gamperl

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The pharmaceutical companies are getting more inclined towards patient support programs (PSPs) which assist patients and/or healthcare professionals (HCPs) in more desirable disease management and cost-effective treatment. The utmost objective of these programs is patient care. The PSPs may include financial assistance to patients, medicine compliance programs, access to HCPs via phone or online chat centers, etc. The PSP has a crucial role in terms of customer acquisition and retention strategies. During the conduct of these programs, Marketing Authorisation Holder (MAH) may receive information related to concerned medicinal products, which is usually reported by patients or involved HCPs. This information may include suspected adverse reaction(s) during/after administration of medicinal products. Hence, the MAH should design PSP to comply with regulatory reporting requirements and avoid non-compliance during PV inspection. The emergence of wireless health devices is lowering the burden on patients to manually incorporate safety data, and building a significant option for patients to observe major swings in reference to drug safety. Therefore, to enhance the adoption of these programs, MAH not only needs to aware patients about advantages of the program, but also recognizes the importance of time of patients and commitments made in a constructive manner. It is indispensable that strengthening the public health is considered as the topmost priority in such programs, and the MAH is compliant to Pharmacovigilance (PV) requirements along with regulatory obligations.

Keywords: drug safety, good pharmacovigilance practice, patient support program, pharmacovigilance

Procedia PDF Downloads 297

Authors: Shuo Mu, Guangzhi Jiang, Jinsa Chen

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The analysis of Indel for RNA sequencing of clinical samples is easily affected by sequencing experiment errors and software selection. In order to improve the efficiency and accuracy of analysis, we developed an automatic reporting system for Indel recognition and annotation based on image snapshot of transcriptome reads alignment. This system includes sequence local-assembly and realignment, target point snapshot, and image-based recognition processes. We integrated high-confidence Indel dataset from several known databases as a training set to improve the accuracy of image processing and added a bioinformatical processing module to annotate and filter Indel artifacts. Subsequently, the system will automatically generate data, including data quality levels and images results report. Sanger sequencing verification of the reference Indel mutation of cell line NA12878 showed that the process can achieve 83% sensitivity and 96% specificity. Analysis of the collected clinical samples showed that the interpretation accuracy of the process was equivalent to that of manual inspection, and the processing efficiency showed a significant improvement. This work shows the feasibility of accurate Indel analysis of clinical next-generation sequencing (NGS) transcriptome. This result may be useful for RNA study for clinical samples with microsatellite instability in immunotherapy in the future.

Keywords: automatic reporting, indel, next-generation sequencing, NGS, transcriptome

Procedia PDF Downloads 170

Authors: S. Shankar Bharathi

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Inspection of surface defects on metallic components has always been challenging due to its specular property. Occurrences of defects such as scratches, rust, pitting are very common in metallic surfaces during the manufacturing process. These defects if unchecked can hamper the performance and reduce the life time of such component. Many of the conventional image processing algorithms in detecting the surface defects generally involve segmentation techniques, based on thresholding, edge detection, watershed segmentation and textural segmentation. They later employ other suitable algorithms based on morphology, region growing, shape analysis, neural networks for classification purpose. In this paper the work has been focused only towards detecting scratches. Global and other thresholding techniques were used to extract the defects, but it proved to be inaccurate in extracting the defects alone. However, this paper does not focus on comparison of different segmentation techniques, but rather describes a novel approach towards segmentation combined with hausdorff dilation distance. The proposed algorithm is based on the distribution of the intensity levels, that is, whether a certain gray level is concentrated or evenly distributed. The algorithm is based on extraction of such concentrated pixels. Defective images showed higher level of concentration of some gray level, whereas in non-defective image, there seemed to be no concentration, but were evenly distributed. This formed the basis in detecting the defects in the proposed algorithm. Hausdorff dilation distance based on mathematical morphology was used to strengthen the segmentation of the defects.

Keywords: metallic surface, scratches, segmentation, hausdorff dilation distance, machine vision

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Authors: Mohamed Ahmed Khali

Abstract:

Numbers of deep well anode ground beds (GBs) have been retrieved due to un operated anode chains. New identical magnetite anode chains(MAC) have been installed at Raslanuf complex impressed current Cathodic protection(ICCP) system, distributed at different plants(Utility, ethylene and polyethylene). All problems associated with retrieving and installation of MACs have been discussed, rectified and presented. All GB associated severely corroded wellhead casings were well maintained and/ or replaced by new fabricated and modified ones. The main cause of wellhead casings internal corrosion was discussed, and the conducted remedy action to overcome future corrosion problem is presented. All GB connected anode junction boxes (AJBs) and shunts were closely inspected, maintained, and necessary replacement/and or modification were carried out on shunts. All damaged GB concrete foundations (CF) have been inspected and completely replaced. All GB associated Transformer-Rectifiers units (TRUs) were subjected to through inspection, and necessary maintenance has been performed on each individual TRU. After completion of all MACs and TRU maintenance activities, each cathodic protection station (CPS) has been re-operated. An alternative current (AC), direct current (DC), voltage and structure to soil potential (S/P) measurements have been conducted, recorded, and all obtained test results are presented. DC current outputs has been adjusted, and DC current outputs of each MAC has been recorded for each GB AJB.

Keywords: magnatite anode, deep well, ground bed, cathodic protection, transformer rectifies, impreced current, junction box

Procedia PDF Downloads 88

Authors: Giovanni Masala, Stefania Marica

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Forecasting electricity load plays a crucial role regards decision making and planning for economical purposes. Besides, in the light of the recent privatization and deregulation of the power industry, the forecasting of future electricity load turned out to be a very challenging problem. Empirical data about electricity load highlights a clear seasonal behavior (higher load during the winter season), which is partly due to climatic effects. We also emphasize the presence of load periodicity at a weekly basis (electricity load is usually lower on weekends or holidays) and at daily basis (electricity load is clearly influenced by the hour). Finally, a long-term trend may depend on the general economic situation (for example, industrial production affects electricity load). All these features must be captured by the model. The purpose of this paper is then to build an hourly electricity load model. The deterministic component of the model requires non-linear regression and Fourier series while we will investigate the stochastic component through econometrical tools. The calibration of the parameters’ model will be performed by using data coming from the Italian market in a 6 year period (2007- 2012). Then, we will perform a Monte Carlo simulation in order to compare the simulated data respect to the real data (both in-sample and out-of-sample inspection). The reliability of the model will be deduced thanks to standard tests which highlight a good fitting of the simulated values.

Keywords: ARMA-GARCH process, electricity load, fitting tests, Fourier series, Monte Carlo simulation, non-linear regression

Procedia PDF Downloads 387

Authors: Satya Pradhan, Venky Nanniyur

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As the software industry transitions from a license-based model to a subscription-based Software-as-a-Service (SaaS) model, many software development groups are using a hybrid development model that incorporates Agile and Waterfall methodologies in different parts of the organization. The traditional metrics used for measuring software quality in Waterfall or Agile paradigms do not apply to this new hybrid methodology. In addition, to respond to higher quality demands from customers and to gain a competitive advantage in the market, many companies are starting to prioritize quality as a strategic differentiator. As a result, quality metrics are included in the decision-making activities all the way up to the executive level, including board of director reviews. This paper presents key challenges associated with measuring software quality in organizations using the hybrid development model. We introduce a framework called Prevention-Inspection-Evaluation-Removal (PIER) to provide a comprehensive metric definition for hybrid organizations. The framework includes quality measurements, quality enforcement, and quality decision points at different organizational levels and project milestones. The metrics framework defined in this paper is being used for all Cisco systems products used in customer premises. We present several field metrics for one product portfolio (enterprise networking) to show the effectiveness of the proposed measurement system. As the results show, this metrics framework has significantly improved in-process defect management as well as field quality.

Keywords: quality management system, quality metrics framework, quality metrics, agile, waterfall, hybrid development system

Procedia PDF Downloads 160

Authors: Hadjer Didouh, Izzaddine Sameut Bouhaik, Mohammed Hadj Meliani

Abstract:

This research delves into the intricate dynamics of biofilm adhesion on surfaces, particularly focusing on the widely employed X52 surface in oil and gas industry pipelines. Biofilms, characterized by microorganisms within a self-produced matrix, pose significant challenges due to their detrimental impact on surfaces. Our study integrates advanced molecular techniques and cutting-edge microscopy, such as scanning electron microscopy (SEM), to identify microbial communities and visually assess biofilm adhesion. Simultaneously, we concentrate on the X52 surface, utilizing impedance spectroscopy and potentiodynamic polarization to gather electrochemical responses under various conditions. In conjunction with the broader investigation, we propose a novel approach to mitigate biofilm-induced corrosion challenges. This involves environmentally friendly inhibitors derived from plants, offering a sustainable alternative to conventional chemical treatments. Our inquiry screens and selects inhibitors based on their efficacy in hindering biofilm formation and reducing corrosion rates on the X52 surface. This study contributes valuable insights into the interplay between electrochemical processes and biofilm attachment on the X52 surface. Furthermore, the outcomes of this research have broader implications for the oil and gas industry, where biofilm-related corrosion is a persistent concern. The exploration of eco-friendly inhibitors not only holds promise for corrosion control but also aligns with environmental considerations and sustainability goals. The comprehensive nature of this research aims to enhance our understanding of biofilm dynamics, provide effective strategies for corrosion mitigation, and contribute to sustainable practices in pipeline management within the oil and gas sector.

Keywords: bio-corrosion, biofilm, attachment, X52, metal/bacteria interface

Procedia PDF Downloads 36

Authors: Keyvan Kashkouli Nejad, Motoaki Sugiura, Atsushi Sato, Takayuki Nozawa, Hyeonjeong Jeong, Sugiko Hanawa , Yuka Kotozaki, Ryuta Kawashima

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The perception of agency/control is altered with presence of discrepancies in the environment or mismatch of predictions (of possible results) and actual results the sense of agency might become altered. Synofzik et al. proposed a two layer model of agency: In the first layer, the Feeling of Agency (FoA) is not directly available to awareness; a slight mismatch in the environment/outcome might cause alterations in FoA, while the agent still feels in control. If the discrepancy passes a threshold, it becomes available to consciousness and alters Judgment of Agency (JoA), which is directly available in the person’s awareness. Most experiments so far only investigate subjects rather conscious JoA, while FoA has been neglected. In this experiment we target FoA by using subliminal discrepancies that can not be consciously detectable by the subjects. Here, we explore whether we can detect this two level model in the subjects behavior and then try to map this in their brain activity. To do this, in a fMRI study, we incorporated both consciously detectable mismatching between action and result and also subliminal discrepancies in the environment. Also, unlike previous experiments where subjective questions from the participants mainly trigger the rather conscious JoA, we also tried to measure the rather implicit FoA by asking participants to rate their performance. We compared behavioral results and also brain activation when there were conscious discrepancies and when there were subliminal discrepancies against trials with no discrepancies and against each other. In line with our expectations, conditions with consciously detectable incongruencies triggered lower JoA ratings than conditions without. Also, conditions with any type of discrepancies had lower FoA ratings compared to conditions without. Additionally, we found out that TPJ and angular gyrus in particular to have a role in coding of JoA and also FoA.

Keywords: agency, fMRI, TPJ, two layer model

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Authors: Timothy E. Frank, Josh R. Aldred, Sophie B. Boulware, Michelle K. Cabonce, Justin H. White

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Materials degrade at different rates in different environments depending on factors such as temperature, aridity, salinity, and solar radiation. Therefore, predicting asset longevity depends, in part, on the environmental conditions to which the asset is exposed. Heating, ventilation, and air conditioning (HVAC) systems are critical to building operations yet are responsible for a significant proportion of their energy consumption. HVAC energy use increases substantially with slight operational inefficiencies. Understanding the environmental influences on HVAC degradation in detail will inform maintenance schedules and capital investment, reduce energy use, and increase lifecycle management efficiency. HVAC inspection records spanning 14 years from 21 locations across the United States were compiled and associated with the climate conditions to which they were exposed. Three environmental features were explored in this study: average high temperature, average low temperature, and annual precipitation, as well as four non-environmental features. Initial insights showed no correlations between individual features and the rate of HVAC component degradation. Using neighborhood component analysis, however, the most critical features related to degradation were identified. Two models were considered, and results varied between them. However, longitude and latitude emerged as potentially the best predictors of average HVAC component degradation. Further research is needed to evaluate additional environmental features, increase the resolution of the environmental data, and develop more robust models to achieve more conclusive results.

Keywords: climate, degradation, HVAC, neighborhood component analysis

Procedia PDF Downloads 413

Authors: Ewa M. Laskowska, Jorn Vatn

Abstract:

Industry 4.0 focuses on digital optimization of industrial processes. The idea is to use extracted data in order to build a decision support model enabling use of those data for real time decision making. In terms of predictive maintenance, the desired decision support tool would be a model enabling prognostics of system's health based on the current condition of considered equipment. Within area of system prognostics and health management, a commonly used health indicator is Remaining Useful Lifetime (RUL) of a system. Because the RUL is a random variable, it has to be estimated based on available health indicators. Health indicators can be of different types and come from different sources. They can be process variables, equipment performance variables, data related to number of experienced failures, etc. The aim of this study is the analysis of performance variables of emergency shutdown valves (ESV) used in oil and gas industry. ESV is inspected periodically, and at each inspection torque and time of valve operation are registered. The data will be analyzed by means of machine learning or statistical analysis. The purpose is to investigate whether the available data could be used as a health indicator for a prognostic purpose. The second objective is to examine what is the most efficient way to incorporate the data into predictive model. The idea is to check whether the data can be applied in form of explanatory variables in Markov process or whether other stochastic processes would be a more convenient to build an RUL model based on the information coming from registered data.

Keywords: emergency shutdown valves, health indicator, prognostics, remaining useful lifetime, RUL

Procedia PDF Downloads 77

Authors: C. Paglia, C. Mosca

Abstract:

Synthetic resin floorsare often used in sport infrastructure. These organic materials are often in contact with a bituminous substrate, which in turn is placed on the ground. In this work, the damage of a basket resin field surface was characterized by means of visual inspection, optical microscopy, resin thickness measurements, adhesion strength, water vapor transmission capacity, capillary water adsorption, granulometry of the bituminous conglomerate, the surface properties, and the water ground infiltration speed. The infiltration speed indicates water pemeability. This was due to its composition: clean sand mixed with gravel. Relatively good adhesion was present between the synthetic resin and the bituminous layer. The adhesion resistance of the bituminous layer was relatively low. According to the required bitumoniousasphalt-concrete mixes AC 11 S, the placed material was more porous. Insufficient constipation was present. The spaces values were above the standard limits, while the apparent densities were lower compared to the conventional AC 11 mixtures. The microstructure outlines the high permeability and porosity of the bituminous layer. The synthetic resin wasvapourproof and did not exhibit capillary adsorption. It exhibited a lower thickness as required, and no multiple placing steps were observed. Multiple cavities were detected along with the interface between the bituminous layer and the resin coating with no intermediate layers. The layer for the pore filling in the bituminous surface was not properly applied. The swelling bubbles on the synthetic pavement were caused by the humidity in the bituminous layer. Water or humidity were present prior to the application of the resin, and the effect was worsened by the upward movement of the water from the ground.

Keywords: resin, floor, damage, durability

Procedia PDF Downloads 152

Authors: Mohamed Ahmed Khalil

Abstract:

The number of deep well anode ground beds (GBs) have been retrieved due to unoperated anode chains. New identical magnetite anode chains (MAC) have been installed at Raslanuf complex impressed current Cathodic protection (ICCP) system, distributed at different plants (Utility, ethylene and polyethylene). All problems associated with retrieving and installation of MACs have been discussed, rectified and presented. All GB-associated severely corroded wellhead casings were well maintained and/or replaced by new fabricated and modified ones. The main cause of the wellhead casing's severe internal corrosion was discussed and the conducted remedy action to overcome future corrosion problems is presented. All GB-connected anode junction boxes (AJBs) and shunts were closely inspected, maintained and necessary replacement and/or modifications were carried out on shunts. All damaged GB concrete foundations (CF) have been inspected and completely replaced. All GB-associated Transformer-Rectifiers Units (TRU) were subjected to thorough inspection and necessary maintenance was performed on each individual TRU. After completion of all MACs and TRU maintenance activities, each cathodic protection station (CPS) has been re-operated, alternative current (AC), direct current (DC), voltage and structure to soil potential (S/P) measurements have been conducted, recorded and all obtained test results are presented. DC current outputs have been adjusted and DC current outputs of each MAC have been recorded for each GB AJB.

Keywords: magnetite anodes, deep well, ground beds, cathodic protection, transformer rectifier, impressed current, junction boxes

Procedia PDF Downloads 104

Authors: Daudi S. Simbeye, Mbazingwa E. Mkiramweni

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Plant diseases have the potential to drastically diminish the quantity and quality of agricultural products. Guava (Psidium guajava), sometimes known as the apple of the tropics, is one of the most widely cultivated fruits in tropical regions. Monitoring plant health and diagnosing illnesses is an essential matter for sustainable agriculture, requiring the inspection of visually evident patterns on plant leaves and fruits. Due to minor variations in the symptoms of various guava illnesses, a professional opinion is required for disease diagnosis. Due to improper pesticide application by farmers, erroneous diagnoses may result in economic losses. This study proposes a method that uses artificial intelligence (AI) to detect and classify the most widespread guava plant by comparing images of its leaves and fruits to datasets. ESP32 CAM is responsible for data collection, which includes images of guava leaves and fruits. By comparing the datasets, these image formats are used as datasets to help in the diagnosis of plant diseases through the leaves and fruits, which is vital for the development of an effective automated agricultural system. The system test yielded the most accurate identification findings (99 percent accuracy in differentiating four guava fruit diseases (Canker, Mummification, Dot, and Rust) from healthy fruit). The proposed model has been interfaced with a mobile application to be used by smartphones to make a quick and responsible judgment, which can help the farmers instantly detect and prevent future production losses by enabling them to take precautions beforehand.

Keywords: early identification, guava plants, fruit diseases, deep learning

Procedia PDF Downloads 64

Authors: Konstantinos Sotiriadis, Michael Tupý, Nikol Žižková, Vít Petránek

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The acid attack on cement mortars modified with rubber aggregates and EVA polymer binder was studied. Mortar specimens were prepared using a type CEM I 42.5 Portland cement and siliceous sand, as well as by substituting 25% of sand with shredded used automobile tires, and by adding EVA polymer in two percentages (5% and 10% of cement mass). Some specimens were only air cured, at laboratory conditions, and their compressive strength and water absorption were determined. The rest specimens were stored in acid solutions (HCl, H2SO4, HNO3) after 28 days of initial curing, and stored at laboratory temperature. Compressive strength tests, mass measurements and visual inspection took place for 28 days. Compressive strength and water absorption of the air-cured specimens were significantly decreased when rubber aggregates are used. The addition of EVA polymer further reduced water absorption, while had no important impact on strength. Compressive strength values were affected in a greater extent by hydrochloric acid solution, followed by sulfate and nitric acid solutions. The addition of EVA polymer decreased compressive strength loss for the specimens with rubber aggregates stored in hydrochloric and nitric acid solutions. The specimens without polymer binder showed similar mass loss, which was higher in sulfate acid solution followed by hydrochloric and nitric acid solutions. The use of EVA polymer delayed mass loss, while its content did not affect it significantly.

Keywords: acid attack, mortar, EVA polymer, rubber aggregates

Procedia PDF Downloads 276

Authors: Miranda I. Dosunmu, Orok E. Oyo-Ita, Inyang O. Oyo-Ita

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Polycyclic aromatic hydrocarbons (PAHs) are a class of priority listed organic pollutants due to their carcinogenicity, mutagenity, acute toxicity and persistency in the environment. The distribution and historical changes of PAHs contamination in recent sediment cores from the Imo River were investigated using gas chromatography coupled with mass spectrometer. The concentrations of total PAHs (TPAHs) ranging from 402.37 ng/g dry weight (dw) at the surface layer of the Estuary zone (ESC6; 0-5 cm) to 92,388.59 ng/g dw at the near surface layer of the Afam zone (ASC5; 5-10 cm) indicate that PAHs contamination was localized not only between sample sites but also within the same cores. Sediment-depth profiles for the four (Afam, Mangrove, Estuary and illegal Petroleum refinery) cores revealed irregular distribution patterns in the TPAH concentrations except the fact that these levels became maximized at the near surface layers (5-10 cm) corresponding to a geological time-frame of about 1996-2004. This time scale coincided with the period of intensive bunkering and oil pipeline vandalization by the Niger Delta militant groups. Also a general slight decline was found in the TPAHs levels from near the surface layers (5-10 cm) to the most recent top layers (0-5 cm) of the cores, attributable to the recent effort by the Nigerian government in clamping down the illegal activity of the economic saboteurs. Therefore, the recent amnesty period granted to the militant groups should be extended. Although mechanism of perylene formation still remains enigmatic, examination of its distributions down cores indicates natural biogenic, pyrogenic and petrogenic origins for the compound at different zones. Thus, the characteristic features of the Imo River environment provide a means of tracing diverse origins for perylene.

Keywords: perylene, historical trend, distribution, origin, Imo River

Procedia PDF Downloads 241

Authors: Yendo Hu, Xu-Yu Wu, Dylan Oh

Abstract:

GPS-Denied drones open the possibility of indoor applications, including dynamic arial surveillance, inspection, safety enforcement, and discovery. Indoor swarming further enhances these applications in accuracy, robustness, operational time, and coverage. For micro-drones, power management becomes a critical issue, given the battery payload restriction. This paper proposes an application enabling battery replacement solution that extends the micro-drone active phase without human intervention. First, a framework to quantify the effectiveness of a power management solution for a drone fleet is proposed. The operation-to-non-operation ratio, ONR, gives one a quantitative benchmark to measure the effectiveness of a power management solution. Second, a survey was carried out to evaluate the ONR performance for the various solutions. Third, through analysis, this paper proposes a solution tailored to the indoor micro-drone, suitable for swarming applications. The proposed automated battery replacement solution, along with a modified micro-drone architecture, was implemented along with the associated micro-drone. Fourth, the system was tested and compared with the various solutions within the industry. Results show that the proposed solution achieves an ONR value of 31, which is a 1-fold improvement of the best alternative option. The cost analysis shows a manufacturing cost of $25, which makes this approach viable for cost-sensitive markets (e.g., consumer). Further challenges remain in the area of drone design for automated battery replacement, landing pad/drone production, high-precision landing control, and ONR improvements.

Keywords: micro-drone, battery swap, battery replacement, battery recharge, landing pad, power management

Procedia PDF Downloads 96

Authors: Mouna Baassi, Mohamed Moussaoui, Hatim Soufi, Sanchaita RajkhowaI, Ashwani Sharma, Subrata Sinha, Said Belaaouad

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Human Immunodeficiency Virus type 1 protease (HIV-1 PR) is one of the most challenging targets of antiretroviral therapy used in the treatment of AIDS-infected people. The performance of protease inhibitors (PIs) is limited by the development of protease mutations that can promote resistance to the treatment. The current study was carried out using statistics and bioinformatics tools. A series of thirty-three compounds with known enzymatic inhibitory activities against HIV-1 protease was used in this paper to build a mathematical model relating the structure to the biological activity. These compounds were designed by software; their descriptors were computed using various tools, such as Gaussian, Chem3D, ChemSketch and MarvinSketch. Computational methods generated the best model based on its statistical parameters. The model’s applicability domain (AD) was elaborated. Furthermore, one compound has been proposed as efficient against HIV-1 protease with comparable biological activity to the existing ones; this drug candidate was evaluated using ADMET properties and Lipinski’s rule. Molecular Docking performed on Wild Type and Mutant Type HIV-1 proteases allowed the investigation of the interaction types displayed between the proteases and the ligands, Darunavir (DRV) and the new drug (ND). Molecular dynamics simulation was also used in order to investigate the complexes’ stability, allowing a comparative study of the performance of both ligands (DRV & ND). Our study suggested that the new molecule showed comparable results to that of Darunavir and may be used for further experimental studies. Our study may also be used as a pipeline to search and design new potential inhibitors of HIV-1 proteases.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation.

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Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

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Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

Procedia PDF Downloads 121

Authors: Peng Hou

Abstract:

Natural products produced from marine bacteria serve as an immense reservoir for anti-infective drugs and therapeutic agents. Nowadays, heterologous expression of gene clusters of interests has been widely adopted as an effective strategy for natural product discovery. Briefly, the heterologous expression flowchart would be: biosynthetic gene cluster identification, pathway construction and expression, and product detection. However, gene cluster capture using traditional Transformation-associated recombination (TAR) protocol is low-efficient (0.5% positive colony rate). To make things worse, most of these putative new natural products are only predicted by bioinformatics analysis such as antiSMASH, and their corresponding natural products biosynthetic pathways are either not expressed or expressed at very low levels under laboratory conditions. Those setbacks have inspired us to focus on seeking new technologies to efficiently edit and refractor of biosynthetic gene clusters. Recently, two cutting-edge techniques have attracted our attention - the CRISPR-Cas9 and Gibson Assembly. By now, we have tried to pretreat Brevibacillus laterosporus strain genomic DNA with CRISPR-Cas9 nucleases that specifically generated breaks near the gene cluster of interest. This trial resulted in an increase in the efficiency of gene cluster capture (9%). Moreover, using Gibson Assembly by adding/deleting certain operon and tailoring enzymes regardless of end compatibility, the silent construct (~80kb) has been successfully refactored into an active one, yielded a series of analogs expected. With the appearances of the novel molecular tools, we are confident to believe that development of a high throughput mature pipeline for DNA assembly, transformation, product isolation and identification would no longer be a daydream for marine natural product discovery.

Keywords: biosynthesis, CRISPR-Cas9, DNA assembly, refactor, TAR cloning

Procedia PDF Downloads 265

Authors: Tae Bo Jeon

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Korean air force is undertaking a big project to replace prevailing hundreds of old air fighters such as F-4, F-5, KF-16 etc. The task is to develop and produce domestic fighters equipped with 2 complete-type engines each. A large number of engines, however, will be purchased as products from a foreign engine maker. In addition to the fighters themselves, secure the proper number of spare engines serves a significant role in maintaining combat readiness and effectively managing the national defense budget due to high cost. In this paper, we presented a model dynamically updating spare engine requirements. Currently, the military administration purchases all the fighters, engines, and spare engines at acquisition stage and does not have additional procurement processes during the life cycle, 30-40 years. With the assumption that procurement procedure during the operational stage is established, our model starts from the initial estimate of spare engine requirements based on limited information. The model then performs military missions and repair/maintenance works when necessary. During operation, detailed field information - aircraft repair and test, engine repair, planned maintenance, administration time, transportation pipeline between base, field, and depot etc., - should be considered for actual engine requirements. At the end of each year, the performance measure is recorded and proceeds to next year when it shows higher the threshold set. Otherwise, additional engine(s) will be bought and added to the current system. We repeat the process for the life cycle period and compare the results. The proposed model is seen to generate far better results appropriately adding spare engines thus avoiding possible undesirable situations. Our model may well be applied to future air force military operations.

Keywords: DMSMS, operational availability, METRIC, PRS

Procedia PDF Downloads 159

Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

Procedia PDF Downloads 179

Authors: Segun Steven Bodunde

Abstract:

Mudlogging is the continuous analysis of rock cuttings and drilling fluids to ascertain the presence or absence of oil and gas from the formation penetrated by the drilling bit. This research highlighted a case study of Well BSS-99ST from ‘Bisas Field’, Niger Delta, with depth extending from 1950m to 3640m (Measured Depth). It was focused on identifying the lithologies encountered at specified depth intervals and to accurately delineate the targeted potential reservoir on the field and prepare the lithology and Master log. Equipment such as the Microscope, Fluoroscope, spin drier, oven, and chemicals, which includes: hydrochloric acid, chloroethene, and phenolphthalein, were used to check the cuttings for their calcareous nature, for oil show and for the presence of Cement respectively. Gas analysis was done using the gas chromatograph and the Flame Ionization Detector, which was connected to the Total Hydrocarbon Analyzer (THA). Drilling Parameters and Gas concentration logs were used alongside the lithology log to predict and accurately delineate the targeted reservoir on the field. The result showed continuous intercalation of sand and shale, with the presence of small quantities of siltstone at a depth of 2300m. The lithology log was generated using Log Plot software. The targeted reservoir was identified between 3478m to 3510m after inspection of the gas analysis, lithology log, electric logs, and the drilling parameters. Total gas of about 345 units and five Alkane Gas components were identified in the specific depth range. A comparative check with the Gamma ray log from the well further confirmed the lithologic sequence and the accurate delineation of the targeted potential reservoir using mudlogging.

Keywords: mudlogging, chromatograph, drilling fluids, calcareous

Procedia PDF Downloads 141

Authors: Xia Luo, Cheng Zeng

Abstract:

Under the promotion of the Central Committee of the Communist Party of China and the State Council in 2017, Xiong'an New Area is the third crucial new area in China established after Shenzhen and Shanghai. Its constructions' significance lies in mitigating Beijing's non-capital functions and exploring a new mode of optimizing development in densely populated and economically intensive areas. For this purpose, developing underground logistics can assume the role of goods distribution in the capital, relieve the road transport pressure in Beijing-Tianjin-Hebei Urban Agglomeration, adjust and optimize the urban layout and spatial structure of it. Firstly, the construction planning of Xiong'an New Area and underground logistics development are summarized, especially the development status abroad, the development trend, and bottlenecks of underground logistics in China. This paper explores the technicality, feasibility, and necessity of four modes of transportation. There are pneumatic capsule pipeline (PCP) technology, the CargoCap technology, cable hauled mule, and automatic guided vehicle (AGV). The above technical parameters and characteristics are introduced to relevant experts or scholars. Through establishing an indicator system, carrying out a questionnaire survey with the Delphi method, the final suggestion is obtained: China should develop logistics vehicles similar to CargoCap, adopting rail mode and driverless mode. Based on China's temporal and spatial logistics demand and the geographical pattern of Xiong'an New Area, the construction scale, technical parameters, node location, and other vital parameters of underground logistics are planned. In this way, we hope to speed up the new area's construction and the logistics industry's innovation.

Keywords: the Xiong'an new area, underground logistics, contrastive analysis, CargoCap, logistics planning

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Authors: Jisong Ryu, Woosik Lee, Yonggu Jang

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The paper discusses the process of establishing a reliable test bed for verifying the usability of Ground Penetrating Radar (GPR) exploration equipment based on an integrated underground spatial map in Korea. The aim of this study is to construct a test bed consisting of metal and non-metal pipelines to verify the performance of GPR equipment and improve the accuracy of the underground spatial integrated map. The study involved the design and construction of a test bed for metal and non-metal pipe detecting tests. The test bed was built in the SOC Demonstration Research Center (Yeoncheon) of the Korea Institute of Civil Engineering and Building Technology, burying metal and non-metal pipelines up to a depth of 5m. The test bed was designed in both vehicle-type and cart-type GPR-mounted equipment. The study collected data through the construction of the test bed and conducting metal and non-metal pipe detecting tests. The study analyzed the reliability of GPR detecting results by comparing them with the basic drawings, such as the underground space integrated map. The study contributes to the improvement of GPR equipment performance evaluation and the accuracy of the underground spatial integrated map, which is essential for urban planning and construction. The study addressed the question of how to verify the usability of GPR exploration equipment based on an integrated underground spatial map and improve its performance. The study found that the test bed is reliable for verifying the performance of GPR exploration equipment and accurately detecting metal and non-metal pipelines using an integrated underground spatial map. The study concludes that the establishment of a test bed for verifying the usability of GPR exploration equipment based on an integrated underground spatial map is essential. The proposed Korean-style test bed can be used for the evaluation of GPR equipment performance and support the construction of a national non-metal pipeline exploration equipment performance evaluation center in Korea.

Keywords: Korea-style GPR testbed, GPR, metal pipe detecting, non-metal pipe detecting

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Authors: Ashish Agarwal, Vaibhav Singh

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Harmful emissions from oil and gas processing facilities have long remained a matter of concern for governments and environmentalists throughout the world. This paper analyses Oil and Natural Gas Corporation (ONGC) gas processing plant in Hazira, Gujarat, India. It is the largest gas-processing complex in the country designed to process 41MMSCMD sour natural gas & associated sour condensate. The complex, sprawling over an area of approximate 705 hectares is the mother plant for almost all industries at Hazira and enroute Hazira Bijapur Jagdishpur pipeline. Various sources of pollution from each unit starting from Gas Terminal to Dew Point Depression unit and Caustic Wash unit along the processing chain were examined with the help of different emission data obtained from ONGC. Pollution discharged to the environment was classified into Water, Air, Hazardous Waste and Solid (Non-Hazardous) Waste so as to analyze each one of them efficiently. To protect air environment, Sulphur recovery unit along with automatic ambient air quality monitoring stations, automatic stack monitoring stations among numerous practices were adopted. To protect water environment different effluent treatment plants were used with due emphasis on aquaculture of the nearby area. Hazira plant has obtained the authorization for handling and disposal of five types of hazardous waste. Most of the hazardous waste were sold to authorized recyclers and the rest was given to Gujarat Pollution Control Board authorized vendors. Non-Hazardous waste was also handled with an overall objective of zero negative impact on the environment. The effect of methods adopted is evident from emission data of the plant which was found to be well under Gujarat Pollution Control Board limits.

Keywords: sulphur recovery unit, effluent treatment plant, hazardous waste, sour gas

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Authors: Fangyan Li, Lin Min Lee, Hui Zhu Peh, Shoet Harn Chan

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Advantame, a derivative of aspartame, is the latest addition to a family of low caloric and high potent dipeptide sweeteners which include aspartame, neotame and alitame. The use of advantame as a high-intensity sweetener in food was first accepted by Food Standards Australia New Zealand in 2011 and subsequently by US and EU food authorities in 2014, with the results from toxicity and exposure studies showing advantame poses no safety concern to the public at regulated levels. To our knowledge, currently there is barely any detailed information on the analytical method of advantame in food matrix, except for one report published in Japanese, stating a high performance liquid chromatography (HPLC) and liquid chromatography/ mass spectrometry (LC-MS) method with a detection limit at ppm level. However, the use of acid in sample preparation and instrumental analysis in the report raised doubt over the reliability of the method, as there is indication that stability of advantame is compromised under acidic conditions. Besides, the method may not be suitable for analyzing food matrices containing advantame at low ppm or sub-ppm level. In this presentation, a simple, specific and sensitive method for the determination of advantame in food is described. The method involved extraction with water and clean-up via solid phase extraction (SPE) followed by detection using liquid chromatography tandem mass spectrometry (LC-MS/MS) in negative electrospray ionization mode. No acid was used in the entire procedure. Single laboratory validation of the method was performed in terms of linearity, precision and accuracy. A low detection limit at ppb level was achieved. Satisfactory recoveries were obtained using spiked samples at three different concentration levels. This validated method could be used in the routine inspection of the advantame level in food.

Keywords: advantame, food, LC-MS/MS, sweetener

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Authors: M. A. García, J. Vinolas, A. Hernando

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Steel is nowadays one of the most important structural materials because of its outstanding mechanical properties. Therefore, in order to look for a sustainable economic model and to optimize the use of extensive resources, new methods to monitor and prevent failure of steel-based facilities are required. The classical mechanical tests, as for instance building tasting, are invasive and destructive. Moreover, for facilities where the steel element is embedded, (as reinforced concrete) these techniques are directly non applicable. Hence, non-invasive monitoring techniques to prevent failure, without altering the structural properties of the elements are required. Among them, electromagnetic methods are particularly suitable for non-invasive inspection of the mechanical state of steel-based elements. The magnetoelastic coupling effects induce a modification of the electromagnetic properties of an element upon applied stress. Since most steels are ferromagnetic because of their large Fe content, it is possible to inspect their structure and state in a non-invasive way. We present here a distinct electromagnetic method for contactless evaluation of internal stress in steel-based elements. In particular, this method relies on measuring the magnetic induction between two coils with the steel specimen in between them. We found that the alteration of electromagnetic properties of the steel specimen induced by applied stress-induced changes in the induction allowed us to detect stress well below half of the elastic limit of the material. Hence, it represents an outstanding non-invasive method to prevent failure in steel-based facilities. We here describe the theoretical model, present experimental results to validate it and finally we show a practical application for detection of stress and inhomogeneities in train railways.

Keywords: magnetoelastic, magnetic induction, mechanical stress, steel

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Authors: Ruqaiya Khalil, Saman Usmani, Zaheer Ul-Haq

Abstract:

The accurate characterization of ligand binding affinity is indispensable for designing molecules with optimized binding affinity. Computational tools help in many directions to predict quantitative correlations between protein-ligand structure and their binding affinities. Molecular dynamics (MD) simulation is a modern state-of-the-art technique to evaluate the underlying basis of ligand-protein interactions by characterizing dynamic and energetic properties during the event. Autoimmune diseases arise from an abnormal immune response of the body against own tissues. The current regimen for the described condition is limited to immune-modulators having compromised pharmacodynamics and pharmacokinetics profiles. One of the key player mediating immunity and tolerance, thus invoking autoimmunity is Interleukin-2; a cytokine influencing the growth of T cells. Molecular dynamics simulation techniques are applied to seek insight into the inhibitory mechanisms of newly synthesized compounds that manifested immunosuppressant potentials during in silico pipeline. In addition to estimation of free energies associated with ligand binding, MD simulation yielded us a great deal of information about ligand-macromolecule interactions to evaluate the pattern of interactions and the molecular basis of inhibition. The present study is a continuum of our efforts to identify interleukin-2 inhibitors of both natural and synthetic origin. Herein, we report molecular dynamics simulation studies of Interluekin-2 complexed with different antagonists previously reported by our group. The study of protein-ligand dynamics enabled us to gain a better understanding of the contribution of different active site residues in ligand binding. The results of the study will be used as the guide to rationalize the fragment based synthesis of drug-like interleukin-2 inhibitors as immune-modulators.

Keywords: immuno-modulators, MD simulation, protein-ligand interaction, structure-based drug design

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Authors: Gozel Judakova, Markus Bause

Abstract:

We present and analyze reliable numerical techniques for simulating complex flow and transport phenomena related to natural gas transportation in pipelines. Such kind of problems are of high interest in the field of petroleum and environmental engineering. Modeling and understanding natural gas flow and transformation processes during transportation is important for the sake of physical realism and the design and operation of pipeline systems. In our approach a two fluid flow model based on a system of coupled hyperbolic conservation laws is considered for describing natural gas flow undergoing hydratization. The accurate numerical approximation of two-phase gas flow remains subject of strong interest in the scientific community. Such hyperbolic problems are characterized by solutions with steep gradients or discontinuities, and their approximation by standard finite element techniques typically gives rise to spurious oscillations and numerical artefacts. Recently, stabilized and discontinuous Galerkin finite element techniques have attracted researchers’ interest. They are highly adapted to the hyperbolic nature of our two-phase flow model. In the presentation a streamline upwind Petrov-Galerkin approach and a discontinuous Galerkin finite element method for the numerical approximation of our flow model of two coupled systems of Euler equations are presented. Then the efficiency and reliability of stabilized continuous and discontinous finite element methods for the approximation is carefully analyzed and the potential of the either classes of numerical schemes is investigated. In particular, standard benchmark problems of two-phase flow like the shock tube problem are used for the comparative numerical study.

Keywords: discontinuous Galerkin method, Euler system, inviscid two-fluid model, streamline upwind Petrov-Galerkin method, twophase flow

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Authors: Norhan H. Mahdally, Bathini Thissera Riham A. ElShiekh, Noha M. Elhosseiny, Mona T. Kashef, Ali M. El Halawany, Mostafa E. Rateb, Ahmed S. Attia

Abstract:

Multidrug-resistant (MDR) pathogens pose a global threat to healthcare settings. The exhaustion of the current antibiotic arsenal and the scarcity of new antimicrobials in the pipeline aggravate this threat and necessitate a prompt and effective response. This study focused on two major pathogens that can cause serious infections: carbapenem-resistant Acinetobacter baumannii (CRAB) and methicillin-resistant Staphylococcus aureus (MRSA). Multiple soil isolates were collected from several locations throughout Egypt and screened for their conventional and non-conventional antimicrobial activities against MDR pathogens. One isolate exhibited potent antimicrobial activity and was subjected to multiple rounds of fractionation. After fermentation and bio-guided fractionation, we identified pure microbial secondary metabolites with two scaffolds that exhibited promising effects against CRAB and MRSA. Scaling up and chemical synthesis of derivatives of the identified metabolite resulted in obtaining a more potent derivative, which we designated as 2HP. Cytotoxicity studies indicated that 2HP is well-tolerated by human cells. Ongoing work is focusing on formulating the new compound into a nano-formulation to enhance its delivery. Also, to have a better idea about how this compound works, a proteomic approach is currently underway. Our findings suggest that 2HP is a potential new broad-spectrum antimicrobial agent. Further studies are needed to confirm these findings and to develop 2HP into a safe and effective treatment for MDR infections.

Keywords: broad-spectrum antimicrobials, carbapenem-resistant acinetobacter baumannii, drug discovery, methicillin-resistant staphylococcus aureus, multidrug-resistant, natural products

Procedia PDF Downloads 65