Search results for: genome mining

Authors: Moti Zwilling, Srečko Natek

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This paper aims to present an innovative predictive analytics analysis in order to find the best combination between two consumers who strive to find their partner or in internet sites. The methodology shown in this paper is based on analysis of consumer preferences and involves data mining and machine learning search techniques. The study is composed of two parts: The first part examines by means of descriptive statistics the correlations between a set of parameters that are taken between man and women where they intent to meet each other through the social media, usually the internet. In this part several hypotheses were examined and statistical analysis were taken place. Results show that there is a strong correlation between the affiliated attributes of man and woman as long as concerned to how they present themselves in a social media such as "Facebook". One interesting issue is the strong desire to develop a serious relationship between most of the respondents. In the second part, the authors used common data mining algorithms to search and classify the most important and effective attributes that affect the response rate of the other side. Results exhibit that personal presentation and education background are found as most affective to achieve a positive attitude to one's profile from the other mate.

Keywords: dating sites, social networks, machine learning, decision trees, data mining

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Authors: Sidharth Talan, Sanjay Kumar Sharma, Eoin Joseph Wallace, Nikita Agrawal

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Underground mining is at the core of rapidly evolving metals and minerals sector due to the increasing mineral consumption globally. Even though the surface mines are still more abundant on earth, the scales of industry are slowly tipping towards underground mining due to rising depth and complexities of orebodies. Thus, the efficient and productive functioning of underground operations depends significantly on the synchronized performance of key elements such as operating site, mining equipment, manpower and mine services. Production drilling is the process of conducting long hole drilling for the purpose of charging and blasting these holes for the production of ore in underground metal mines. Thus, production drilling is the crucial segment in the underground metal mining value chain. This paper presents the process mapping tool to evaluate the production drilling process in the underground metal mining operation by dividing the given process into three segments namely Input, Process and Output. The three segments are further segregated into factors and sub-factors. As per the study, the major input factors crucial for the efficient functioning of production drilling process are power, drilling water, geotechnical support of the drilling site, skilled drilling operators, services installation crew, oils and drill accessories for drilling machine, survey markings at drill site, proper housekeeping, regular maintenance of drill machine, suitable transportation for reaching the drilling site and finally proper ventilation. The major outputs for the production drilling process are ore, waste as a result of dilution, timely reporting and investigation of unsafe practices, optimized process time and finally well fragmented blasted material within specifications set by the mining company. The paper also exhibits the drilling loss matrix, which is utilized to appraise the loss in planned production meters per day in a mine on account of availability loss in the machine due to breakdowns, underutilization of the machine and productivity loss in the machine measured in drilling meters per unit of percussion hour with respect to its planned productivity for the day. The given three losses would be essential to detect the bottlenecks in the process map of production drilling operation so as to instigate the action plan to suppress or prevent the causes leading to the operational performance deficiency. The given tool is beneficial to mine management to focus on the critical factors negatively impacting the production drilling operation and design necessary operational and maintenance strategies to mitigate them. 

Keywords: process map, drilling loss matrix, SIPOC, productivity, percussion rate

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Authors: G. Gevorgyan, S. Khudaverdyan, A. Vaseashta

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The Lake Sevan basin is situated in the eastern part of the Republic of Armenia (Gegharquniq marz/district). The heavy metal pollution of the some tributaries of Lake Sevan was investigated. Water sampling was performed in August and December, 2014 from the 4 observation sites: 1) Sotq river upstream (about 600 meters upstream from the Sotq gold mine); 2) Sotq river mouth; 3) Masrik river mouth; 4) Dzknaget river mouth. Heavy metal (V, Fe, Ni, Cu, As, Mo, Pb) concentrations in the water samples were determined by the standard methods using an atomic absorption spectrophotometer. The results of the study showed that heavy metal content mainly increased from the upstream of the Sotq river to the mouth of the Masrik river which may have been conditioned by the influence of gold mining activity as the Masrik and its tributary-Sotq rivers passing through the gold mining area were exposed to heavy metal pollution. The observation sites can be ranked by pollution degree as follows: №3> №2> №1> №4. The highest heavy metal pollution degree was observed in the Masrik river mouth which may have been conditioned by the direct impact of gold mining activity and the pressure of its tributary–the Sotq river which flows through the gold mining area. The lowest heavy metal pollution degree was registered in the Dzknaget river mouth which flowing through rural areas wasn’t subject to significant heavy metal pollution. According to the observation sites of the Sotq and Masrik rivers, high positive correlation was mainly observed between the concentrations of the investigated heavy metals (except nickel) which indicated that all the heavy metals except the nickel had the same anthropogenic pollution source which was the activity of the Sotq gold mine. In general, it is possible to state that the activity of the Sotq gold mine in the Lake Sevan basin caused the heavy metal pollution of the Sotq and Masrik rivers which may have posed environmental hazards. Heavy metals are nondegradable substances, and heavy metal pollution of freshwater systems may pose risks to the environment and human health through accumulation in the tissues of aquatic organisms, water-food chain as well as oral ingestion and dermal contact.

Keywords: Armenia, Lake Sevan basin, gold mining activity, river ecosystems, heavy metal pollution

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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: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: Chamilani Nikapitiya, Mahanama De Zoysa, Jehee Lee

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Most of the bacterial diseases are associated with high mortalities in aquaculture species and causing huge economic losses. Different approaches have been taken to prevent or control of bacterial diseases including use of vaccines, probiotics, chemotherapy, water quality management, etc. Antibiotics are widely applying as chemotherapy to control bacterial diseases, however, it has been shown that frequent use of antibiotics is favored to develop multi-drug resistance bacteria. Therefore, phages and phage encoded lytic proteins are known to be one of the most promising alternatives for antibiotics to avoid the emergence of antibiotic-resistant bacteria. We isolated and characterized the two lytic phages, namely pAh-1 and pAs-1 against pathogenic Aeromonas hydrophila and Aeromonas salmonicida, respectively. Morphological characteristics were analyzed by Transmission electron microscopy (TEM) and host strain specificities were tested with Aeromonas and other closely related bacterial strains. TEM analysis revealed that both pAh-1 and pAsm-1 are composed of an icosahedral head and a segmented tail, and we suggest that, they are new members of Myoviridae family. Genome sizes of isolated phages were estimated by restriction enzyme digestion of genomic DNA using selected endonucleases followed by agarose gel electrophoresis. Estimated genome size of pAh-1 and pAs-1 were approximately 64 Kbp and 120 Kbp, respectively. Both pAh-1 and pAs-1 have shown narrow host specificity. Moreover, protective effects of phage therapy against fish pathogenic A. hydrophila were investigated in zebrafish model. The survival rate was 40% higher when zebrafish received intra-peritoneal injection (i.p.) of pAh-1 were simultaneously challenge A. hydrophila (2 x 106 CFU/fish) compared to that without phage treatment. Overall results suggest that both pAh-1 and pAs-1 can be used as a potential phage therapy to control Aeromonas infections in aquaculture.

Keywords: Aeromonas infections, antibiotic resistance, bacteriophage, bio-control, lytic phage

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Authors: Hoda Ghavamipoor, S. Alireza Hashemi Golpayegani

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An approach to model the customer interaction with e-commerce websites is presented. Considering the service quality level as a predictive feature, we offer an improved method based on the Customer Behavior Model Graph (CBMG), a state-transition graph model. To derive the Quality of Service sensitive-CBMG (QoS-CBMG) model, process-mining techniques is applied to pre-processed website server logs which are categorized as ‘buy’ or ‘visit’. Experimental results on an e-commerce website data confirmed that the proposed method outperforms CBMG based method.

Keywords: customer behavior model, electronic commerce, quality of service, customer behavior model graph, process mining

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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

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Authors: Soumyadip Banerjee, Tanmoy Maity

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The recovery of power from waste air generated by mine ventilation fans presents a promising avenue for enhancing energy efficiency in mining operations. This abstract explores the feasibility and benefits of utilizing turbine generators to capture the kinetic energy present in waste air and convert it into electrical power. By integrating turbine generator systems into mine ventilation infrastructures, the potential to harness and utilize the previously untapped energy within the waste air stream is realized. This study examines the principles underlying turbine generator technology and its application within the context of mine ventilation systems. The process involves directing waste air from ventilation fans through specially designed turbines, where the kinetic energy of the moving air is converted into rotational motion. This mechanical energy is then transferred to connected generators, which convert it into electrical power. The recovered electricity can be employed for various on-site applications, including powering mining equipment, lighting, and control systems. The benefits of power recovery from waste air using turbine generators are manifold. Improved energy efficiency within the mining environment results in reduced dependence on external power sources and associated cost savings. Additionally, this approach contributes to environmental sustainability by utilizing a previously wasted resource for power generation. Resource conservation is further enhanced, aligning with modern principles of sustainable mining practices. However, successful implementation requires careful consideration of factors such as waste air characteristics, turbine design, generator efficiency, and integration into existing mine infrastructure. Maintenance and monitoring protocols are necessary to ensure consistent performance and longevity of the turbine generator systems. While there is an initial investment associated with equipment procurement, installation, and integration, the long-term benefits of reduced energy costs and environmental impact make this approach economically viable. In conclusion, the recovery of power from waste air from mine ventilation fans using turbine generators offers a tangible solution to enhance energy efficiency and sustainability within mining operations. By capturing and converting the kinetic energy of waste air into usable electrical power, mines can optimize resource utilization, reduce operational costs, and contribute to a greener future for the mining industry.

Keywords: waste to energy, wind power generation, exhaust air, power recovery

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Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

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Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

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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: Bitopi Dutta

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Development Induced Displacement (DID) of subaltern groups has been an issue of intense debate in India. This research will do a gender analysis of displacement induced by the mining projects in tribal indigenous societies of North East India, centering on the primary research question which is 'How does DID reorder gendered relationship in tribal matrilineal societies?' This paper will not focus primarily on the impacts of the displacement induced by coal mining on indigenous tribal women in the North East India; it will rather study 'what' are the processes that lead to these transformations and 'how' do they operate. In doing so, the paper will locate the cracks in traditional social systems that the discourse of displacement manipulates for its own benefit. DID in this sense will not only be understood as only physical displacement, but also as social and cultural displacement. The study will cover one matrilineal tribe in the state of Meghalaya in the North East India affected by several coal mining projects in the last 30 years. In-depth unstructured interviews used to collect life narratives will be the primary mode of data collection because the indigenous culture of the tribes in Meghalaya, including the matrilineal tribes, is based on oral history where knowledge and experiences produced under a tradition of oral history exist in a continuum. This is unlike modern societies which produce knowledge in a compartmentalized system. An interview guide designed around specific themes will be used rather than specific questions to ensure the flow of narratives from the interviewee. In addition to this, a number of focus groups will be held. The data collected through the life narrative will be supplemented and contextualized through documentary research using government data, and local media sources of the region.

Keywords: displacement, gender-relations, matriliny, mining

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Authors: K. Vrinda

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Coastal ecosystems across the world are facing a lot of challenges due to natural phenomena as well as from uncontrolled human interventions. Here, Alappad, a coastal island situated in Kerala, India is undergoing significant damage and is gradually losing its environmental and social sustainability. The area is blessed with very rare and precious black mineral sand deposits. Sand mining for these minerals started in 1911 and is still continuing. But, unfortunately all the problems that Alappad faces now, have its root on mining of this mineral sand. The land area is continuously diminishing due to sea erosion. The mining has also caused displacement of people and environmental degradation. Marine life also is getting affected by mining on beach and pollution. The inhabitants are fishermen who are largely dependent on the eco-system for a living. So loss of environmental sustainability subsequently affects social sustainability too. Now the damage has reached a point beyond which our actions may not be able to make any impact. This was one of the most affected areas of the 2004 tsunami and the environmental degradation has further increased the vulnerability. So this study focuses on understanding the concerns related to the resource utilization, environment and the indigenous community staying there, and on formulating suitable strategies to restore the sustainability of the area. An extensive study was conducted on site, to find out the physical, social, and economical characteristics of the area. A focus group discussion with the inhabitants shed light on different issues they face in their day-to-day life. The analysis of all these data, led to the formation of a new development vision for the area which focuses on environmental restoration and socio-economic development while allowing controlled exploitation of resources. A participatory approach is formulated which enables these three aspects through community based programs.

Keywords: Community development, Disaster resilience, Ecological restoration, Environmental sustainability, Social-environmental planning, Social Sustainability

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Authors: Habila Nuhu

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Natural radionuclides in the environment can significantly contribute to human exposure to ionizing radiation. The knowledge of their levels in an environment can help the radiological protection agencies in policymaking. Measurement of natural radioactivity in major soils in the tin mining state of Perak Malaysia has been conducted using an HPGe detector. Seventy (70) soil samples were collected at widely distributed locations in the state. Six major soil types were sampled, and thirteen districts around the state were covered. The following were the results of the 226Ra (238U), 228Ra (232Th), and 40K activity in the soil samples: 226Ra (238U) has a mean activity concentration of 191.83 Bq kg⁻¹, more than five times the UNSCEAR reference limits of 35 Bq kg⁻¹. The mean activity concentration of 228Ra (232Th) with a value of 232.41 Bq kg⁻¹ is over seven times the UNSCEAR reference values of 30 Bq kg⁻¹. The average concentration of 40K activity was 275.24 Bq kg⁻¹, which was less than the UNSCEAR reference limit of 400 Bq Kg⁻¹. The range of external hazards index (Hₑₓ) values was from 1.03 to 2.05, while the internal hazards index (Hin) was from 1.48 to 3.08. The Hex and Hin should be less than one for minimal external and internal radiation threats as well as secure use of soil material for building construction. The Hₑₓ and Hin results generally indicate that while using the soil types and their derivatives as building materials in the study area, care must be taken.

Keywords: activity concentration, hazard index, soil samples, tin mining

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Authors: Vahid Bayrami Rad

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In this research, common methods and techniques have been investigated with a focus on intelligent fault finding and monitoring systems in the oil industry. In fact, remote and intelligent control methods are considered a necessity for implementing various operations in the oil industry, but benefiting from the knowledge extracted from countless data generated with the help of data mining algorithms. It is a avoid way to speed up the operational process for monitoring and troubleshooting in today's big oil companies. Therefore, by comparing data mining algorithms and checking the efficiency and structure and how these algorithms respond in different conditions, The proposed (Bayesian) algorithm using data clustering and their analysis and data evaluation using a colored Petri net has provided an applicable and dynamic model from the point of view of reliability and response time. Therefore, by using this method, it is possible to achieve a dynamic and consistent model of the remote control system and prevent the occurrence of leakage in oil pipelines and refineries and reduce costs and human and financial errors. Statistical data The data obtained from the evaluation process shows an increase in reliability, availability and high speed compared to other previous methods in this proposed method.

Keywords: wireless sensors, petroleum equipment troubleshooting, Bayesian algorithm, colored Petri net, rapid miner, data mining-reliability

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Authors: Andrey V. Khromov, Antonida V. Makhotenko, Ekaterina A. Snigir, Svetlana S. Makarova, Natalia O. Kalinina, Valentin V. Makarov, Mikhail E. Taliansky

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Due to its simplicity, CRISPR/Cas9 has become widely used and capable of inducing mutations in the genes of organisms of various kingdoms. The aim of this work was to develop applications for the efficient modification of DNA coding sequences of phytoene desaturase (PDS), coilin and vacuolar invertase (Solanum tuberosum) genes, and to develop a new nanoparticles carrier efficient technology to deliver the CRISPR/Cas9 system for editing the plant genome. For each of the genes - coilin, PDS and vacuolar invertase, five single RNA guide (sgRNAs) were synthesized. To determine the most suitable nanoplatform, two types of NP platforms were used: magnetic NPs (MNPS) and gold NPs (AuNPs). To test the penetration efficiency, they were functionalized with fluorescent agents - BSA * FITS and GFP, as well as labeled Cy3 small-sized RNA. To measure the efficiency, a fluorescence and confocal microscopy were used. It was shown that the best of these options were AuNP - both in the case of proteins and in the case of RNA. The next step was to check the possibility of delivering components of the CRISPR/Cas9 system to plant cells for editing target genes. AuNPs were functionalized with a ribonucleoprotein complex consisting of Cas9 and corresponding to target genes sgRNAs, and they were biolistically bombarded to axillary buds and apical meristems of potato plants. After the treatment by the best NP carrier, potato meristems were grown to adult plants. DNA isolated from this plants was sent to a preliminary fragment of the analysis to screen out the non-transformed samples, and then to the NGS. The present work was carried out with the financial support from the Russian Science Foundation (grant No. 16-16-04019).

Keywords: biobombardment, coilin, CRISPR/Cas9, nanoparticles, NPs, PDS, sgRNA, vacuolar invertase

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Authors: Kobamelo Mashaba

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The molten slag has a high substantial temperatures range between 1723-1923, carrying a huge amount of useful energy for reducing energy consumption and CO₂ emissions under the heat recovery process. Therefore in this study, we investigated the performance of the modified crank Nicolson method for a delayed partial differential equation on the heat recovery of molten slag in the metallurgical mining environment. It was proved that the proposed method converges quickly compared to the classic method with the existence of a unique solution. It was inferred from numerical result that the proposed methodology is more viable and profitable for the mining industry.

Keywords: delayed partial differential equation, modified Crank-Nicolson Method, molten slag, heat recovery, parabolic equation

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Authors: Avinash Vellore Sunder, Shikha Shah, Pramod P. Wangikar

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The enzymatic conversion of nitriles to carboxylic acids by nitrilases has gained significance in the green synthesis of several pharmaceutical precursors and fine chemicals. While nitrilases have been characterized from different sources, the industrial application requires the identification of nitrilases that possess higher substrate tolerance, wider specificity and better thermostability, along with the development of an efficient bioprocess for producing large amounts of nitrilase. To produce large amounts of nitrilase, we developed a fed-batch fermentation process on defined media for the high cell density cultivation of E. coli cells expressing the well-studied nitrilase from Alcaligenes fecalis. A DO-stat feeding approach was employed combined with an optimized post-induction strategy to achieve nitrilase titer of 2.5*105 U/l and 78 g/l dry cell weight. We also identified 16 novel nitrilase sequences from genome mining and analysis of substrate binding residues. The nitrilases were expressed in E. coli and their biocatalytic potential was evaluated on a panel of 22 industrially relevant nitrile substrates using high-throughput screening and HPLC analysis. Nine nitrilases were identified to exhibit high activity on structurally diverse nitriles including aliphatic and aromatic dinitriles, heterocyclic, -hydroxy and -keto nitriles. With fed-batch biotransformation, whole-cell Zobelia galactanivorans nitrilase achieved yields of 2.4 M nicotinic acid and 1.8 M isonicotinic acid from 3-cyanopyridine and 4-cyanopyridine respectively within 5 h, while Cupravidus necator nitrilase enantioselectively converted 740 mM mandelonitrile to (R)–mandelic acid. The nitrilase from Achromobacter insolitus could hydrolyze 542 mM iminodiacetonitrile in 1 h. The availability of highly active nitrilases along with bioprocesses for enzyme production expands the toolbox for industrial biocatalysis.

Keywords: biocatalysis, isonicotinic acid, iminodiacetic acid, mandelic acid, nitrilase

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Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: Maphuti Georgina Kwata

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Coal mining in Mpumalanga Province is known of contributing to the atmospheric pollution from various activities. Gold mining in North-West Province is known of also contributing to the atmospheric pollution especially with the production of radon gas. In this research directional dust deposition gauge was used to measure source of direction and meteorological data was used to determine the wind rose blowing and the influence of the seasonal changes. Fourteen months of dust collection was undertaken in Witbank Area and Carletonville Area. The results shows that the sources of direction for Ericson Dam its East in February 2010 and Tip Area shows that the source of direction its West in October 2010. In the East direction there were mining operations, power stations which contributed to the East to be the sources of direction. In the West direction there were smelters, power stations and agricultural activities which contributed for the source of direction to be the West direction for Driefontein Mine: East Recreational Village Club. The East of Leslie Williams hospital is the source of direction which also indicated that there dust generating activities such as mining operation, agricultural activities. The meteorological results for Emalahleni Area in summer and winter the wind rose blow with wind speed of 5-10 ms-1 from the East sector. Annual average for the wind rose blow its East South eastern sector with 20 ms-1 and day time the wind rose from northwestern sector with excess of 20 ms-1. The night time wind direction East-eastern direction with a maximum wind speed of 20 ms-1. The meteorogical results for Driefontein Mine show that North-western sector and north-eastern sector wind rose is blowing with 5-10 ms-1 win speed. Day time wind blows from the West sector and night time wind blows from the north sector. In summer the wind blows North-east sector with 5-10 ms-1 and winter wind blows from North-west and it’s also predominant. In spring wind blows from north-east. The conclusion is that not only mining operation where the directional dust deposit gauge were installed contributed to the source of direction also the power stations, smelters, and other activities nearby the mining operation contributed. The recommendations are the dust suppressant for unpaved roads should be used on a regular basis and there should be monitoring of the weather conditions (the wind speed and direction prior to blasting to ensure minimal emissions).

Keywords: directional dust deposition gauge, BS part 5 1747 dust deposit gauge, wind rose, wind blowing

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Authors: Leonard Lipovich, Pattaraporn Thepsuwan, Anton-Scott Goustin, Juan Cai, Donghong Ju, James B. Brown

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Two-thirds of human genes do not encode any known proteins. Aside from long non-coding RNA (lncRNA) genes with recently-discovered functions, the ~40,000 non-protein-coding human genes remain poorly understood, and a role for their transcripts as de-facto unconventional messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential, but without independent evidence of proteins from lncRNA open reading frames (ORFs), ribosome binding of lncRNAs does not prove translation. Previously, we mass-spectrometrically documented translation of specific lncRNAs in human K562 and GM12878 cells. We now examined lncRNA translation in human MCF7 cells, integrating strand-specific Illumina RNAseq, Riboseq, and deep mass spectrometry in biological quadruplicates performed at two core facilities (BGI, China; City of Hope, USA). We excluded known-protein matches. UCSC Genome Browser-assisted manual annotation of imperfect (tryptic-digest-peptides)-to-(lncRNA-three-frame-translations) alignments revealed three peptides hypothetically explicable by 'stop-to-nonstop' in-frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24-AS1. To search for this phenomenon genomewide, we designed and implemented a novel pipeline, matching tryptic-digest spectra to wildcard-instead-of-stop versions of repeat-masked, six-frame, whole-genome translations. Along with singleton putative stop-to-nonstop events affecting four other lncRNAs, we identified 24 additional peptides with stop-to-nonstop in-frame substitutions from multiple positive-strand MMP24-AS1 ORFs. Only UAG and UGA, never UAA, stop codons were impacted. All MMP24-AS1-matching spectra met the same significance thresholds as high-confidence known-protein signatures. Targeted resequencing of MMP24-AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencing-detectable RNA editing. This unprecedented apparent gene-specific violation of the genetic code highlights the importance of matching peptides to whole-genome, not known-genes-only, ORFs in mass-spectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome. Funding: NIH Director’s New Innovator Award 1DP2-CA196375 to LL.

Keywords: genetic code, lncRNA, long non-coding RNA, mass spectrometry, proteogenomics, ribo-seq, ribosome, RNAseq

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Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Abdullah Al Farwan, Ya Zhang

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In today’s educational arena, it is critical to understand educational data and be able to evaluate important aspects, particularly data on student achievement. Educational Data Mining (EDM) is a research area that focusing on uncovering patterns and information in data from educational institutions. Teachers, if they are able to predict their students' class performance, can use this information to improve their teaching abilities. It has evolved into valuable knowledge that can be used for a wide range of objectives; for example, a strategic plan can be used to generate high-quality education. Based on previous data, this paper recommends employing data mining techniques to forecast students' final grades. In this study, five data mining methods, Decision Tree, JRip, Naive Bayes, Multi-layer Perceptron, and Random Forest with wrapper feature selection, were used on two datasets relating to Portuguese language and mathematics classes lessons. The results showed the effectiveness of using data mining learning methodologies in predicting student academic success. The classification accuracy achieved with selected algorithms lies in the range of 80-94%. Among all the selected classification algorithms, the lowest accuracy is achieved by the Multi-layer Perceptron algorithm, which is close to 70.45%, and the highest accuracy is achieved by the Random Forest algorithm, which is close to 94.10%. This proposed work can assist educational administrators to identify poor performing students at an early stage and perhaps implement motivational interventions to improve their academic success and prevent educational dropout.

Keywords: classification algorithms, decision tree, feature selection, multi-layer perceptron, Naïve Bayes, random forest, students’ academic performance

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Authors: Diego Rodrigues, Marcelo Lisboa, Elismar Batista, Marcos Dias

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Based on data on child labor, this work arises questions about how to understand and locate the factors that make up the child labor rates, and which properties are important to analyze these cases. Using data mining techniques to discover valid patterns on Brazilian social databases were evaluated data of child labor in the State of Tocantins (located north of Brazil with a territory of 277000 km2 and comprises 139 counties). This work aims to detect factors that are deterministic for the practice of child labor and their relationships with financial indicators, educational, regional and social, generating information that is not explicit in the government database, thus enabling better monitoring and updating policies for this purpose.

Keywords: social data, government decision making, association of social data, data mining

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Authors: Yayun Hsu, Henry Horng-Shing Lu

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In this paper, a new method is proposed to extending the method of connected component labeling from processing binary images to multi-scale modeling of images. By using the adaptive threshold of multi-scale attributes, this approach minimizes the possibility of missing those important components with weak intensities. In addition, the computational cost of this approach remains similar to that of the typical approach of component labeling. Then, this methodology is applied to grain boundary detection and Drosophila Brain-bow neuron segmentation. These demonstrate the feasibility of the proposed approach in the analysis of challenging microscopy images for scientific discovery.

Keywords: microscopic image processing, scientific data mining, multi-scale modeling, data mining

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Authors: Teklu Urgessa, Joong Seek Lee

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Social media is becoming the primary choice of activists to make their voices heard. This fact is coupled by two main reasons. The first reason is the emergence web 2.0, which gave the users opportunity to become content creators than passive recipients. Secondly the control of the mainstream mass media outlets by the governments and individuals with their political and economic interests. This paper aimed at exploring twitter data of network actors talking about the marathon silver medalists on Rio2016, who showed solidarity with the Oromo protesters in Ethiopia on the marathon race finish line when he won silver. The aim is to discover important insight using social network analysis and mining. The hashtag #FeyisaLelisa was used for Twitter network search. The actors’ network was visualized and analyzed. It showed the central influencers during first 10 days in August, were international media outlets while it was changed to individual activist in September. The degree distribution of the network is scale free where the frequency of degrees decay by power low. Text mining was also used to arrive at meaningful themes from tweet corpus about the event selected for analysis. The semantic network indicated important clusters of concepts (15) that provided different insight regarding the why, who, where, how of the situation related to the event. The sentiments of the words in the tweets were also analyzed and indicated that 95% of the opinions in the tweets were either positive or neutral. Overall, the finding showed that Olympic stage protest of the marathoner brought the issue of Oromo protest to the global stage. The new research framework is proposed based for event-based social network analysis and mining based on the practical procedures followed in this research for event-based social media sense making.

Keywords: human rights, Olympics, social media, network analysis, social network ming

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Authors: Nhleko Monique Chiloane

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The gold mining industry has predominantly used ammonium nitrate fuel oil (ANFO) explosives for decades, although these are known to be “gassier” and their detonation results in toxic fumes, for example, carbon monoxide (CO), nitrogen oxides (NOx) and ammonia. Re-entry into underground workings too soon after blasting can lead to fatal exposure to toxic fumes. It is, therefore, required that the polluted air be removed from the affected areas within a reasonable period before employees' re-entry into the working area. Post-blast re-entry times have therefore been described as a productivity bottleneck. The known causes of post-blast fumes are water ingress, incorrect fuel to oxygen ratio, confinement, explosive additives etc. To prevent or minimize post-blast fumes, some researchers have used neutralization, re-burning technique and non-explosive products or different oxidizing agents. The use of commercial explosives without nitrate oxidizing agents can also minimize the production of blasting fumes and thereby reduce the time needed for the clearance of these fumes to allow workers to re-enter the underground workings safely. The reduction in non-production time directly contributes to an increase in the available time per shift for productive work, thus leading to continuous mining. However, owing to its low cost and ease of use, ANFO is still widely used in South African underground blasting operations.

Keywords: post-blast fumes, continuous mining, ammonium nitrate explosive, non-explosive blasting, re-entry period

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Authors: Dewi Juliah Ratnaningsih, Imas Sukaesih Sitanggang

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Classification is one of data mining techniques that aims to discover a model from training data that distinguishes records into the appropriate category or class. Data mining classification methods can be applied in education, for example, to determine the classification of non-active students in Indonesia Open University. This paper presents a comparison of three methods of classification: Naïve Bayes, Bagging, and C.45. The criteria used to evaluate the performance of three methods of classification are stratified cross-validation, confusion matrix, the value of the area under the ROC Curve (AUC), Recall, Precision, and F-measure. The data used for this paper are from the non-active Indonesia Open University students in registration period of 2004.1 to 2012.2. Target analysis requires that non-active students were divided into 3 groups: C1, C2, and C3. Data analyzed are as many as 4173 students. Results of the study show: (1) Bagging method gave a high degree of classification accuracy than Naïve Bayes and C.45, (2) the Bagging classification accuracy rate is 82.99 %, while the Naïve Bayes and C.45 are 80.04 % and 82.74 % respectively, (3) the result of Bagging classification tree method has a large number of nodes, so it is quite difficult in decision making, (4) classification of non-active Indonesia Open University student characteristics uses algorithms C.45, (5) based on the algorithm C.45, there are 5 interesting rules which can describe the characteristics of non-active Indonesia Open University students.

Keywords: comparative analysis, data mining, clasiffication, Bagging, Naïve Bayes, C.45, non-active students, Indonesia Open University

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Authors: Jihyun Song, Kyeongjoo Kim, Minsoo Lee

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Due to the development of information technology and wireless Internet technology, various data are being generated in various fields. These data are advantageous in that they provide real-time information to the users themselves. However, when the data are accumulated and analyzed, more various information can be extracted. In addition, development and dissemination of boards such as Arduino and Raspberry Pie have made it possible to easily test various sensors, and it is possible to collect sensor data directly by using database application tools such as MySQL. These directly collected data can be used for various research and can be useful as data for data mining. However, there are many difficulties in using the board to collect data, and there are many difficulties in using it when the user is not a computer programmer, or when using it for the first time. Even if data are collected, lack of expert knowledge or experience may cause difficulties in data analysis and visualization. In this paper, we aim to construct a library for sensor data collection and analysis to overcome these problems.

Keywords: clustering, data mining, DBSCAN, k-means, k-medoids, sensor data

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Authors: Carla Palencia-Aguilar

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Calculations of Net Carbon Balance can be obtained by means of Net Biome Productivity (NBP), Net Ecosystem Productivity (NEP), and Net Primary Production (NPP). The latter is an important component of the biosphere carbon cycle and is easily obtained data from MODIS MOD17A3HGF; however, the results are only available yearly. To overcome data availability, bands 33 to 36 from MODIS MYD021KM (obtained on a daily basis) were analyzed and compared with NPP data from the years 2000 to 2021 in 7 sites where surface mining takes place in the Colombian territory. Coal, Gold, Iron, and Limestone were the minerals of interest. Scales and Units as well as thermal anomalies, were considered for net carbon balance per location. The NPP time series from the satellite images were filtered by using two Matlab filters: First order and Discrete Transfer. After filtering the NPP time series, comparing the graph results from the satellite’s image value, and running a linear regression, the results showed R2 from 0,72 to 0,85. To establish comparable units among NPP and bands 33 to 36, the Greenhouse Gas Equivalencies Calculator by EPA was used. The comparison was established in two ways: one by the sum of all the data per point per year and the other by the average of 46 weeks and finding the percentage that the value represented with respect to NPP. The former underestimated the total CO2 emissions. The results also showed that coal and gold mining in the last 22 years had less CO2 emissions than limestone, with an average per year of 143 kton CO2 eq for gold, 152 kton CO2 eq for coal, and 287 kton CO2 eq for iron. Limestone emissions varied from 206 to 441 kton CO2 eq. The maximum emission values from unfiltered data correspond to 165 kton CO2 eq. for gold, 188 kton CO2 eq. for coal, and 310 kton CO2 eq. for iron and limestone, varying from 231 to 490 kton CO2 eq. If the most pollutant limestone site improves its production technology, limestone could count with a maximum of 318 kton CO2 eq emissions per year, a value very similar respect to iron. The importance of gathering data is to establish benchmarks in order to attain 2050’s zero emissions goal.

Keywords: carbon dioxide, NPP, MODIS, MINING

Procedia PDF Downloads 87